Here's some feedback on the Shadow Realm itself, as produced by the RMG.
First the good. Great aesthetic! It feels dark, alien and oppressive. (By comparison, so long as you have dark vision, the underground layer feels very open, bright, and high-visibility, which is strange because, of the three layers, you would expect cave tunnels to allow the least visibility. Probably the game should have -1 vision range for everyone underground, and also -1 bonus from dark vision to make the caves feel a lot more like caves. It should probably also have +2 strategic movement cost for everything in caves and for everything on water, but that's off topic.)
The zoomed out paper map isn't as useful as it could be. Some sites (e.g., Hollow Grove) aren't displayed on it. Other sites have icons that are misleading or not very useful. It'd probably be best to make the ubiquitous Shadow Weeds have a distinctive icon that sets them apart, e.g., make them have the same "useless plant" icon that flowers of solace have. It's very odd to have the glass furnaces show up with a plant icon on the map, especially the same plant icon as all the Shadow Weeds. It'd probably make more sense to make them have the "mine" icon like their magma-forge cousins, or at least to make sure that they have a different plant icon from the Shadow Weeds (e.g., by making Shadow Weeds all have the flowers of solace icon). The Celestial Pool is also a highly useful visit structure, but its map icon makes it blend in with all the other 3-window treasure sites -- probably better to give it a visit site icon, either like an angel shrine, or whichever plant icon you don't use for Shadow Weeds.
Topographically, the shadow realm feels quite boring, compared to the other two layers. The main geography differences between shadow realm and surface is that the shadow realm has completely impassible void blocking passage in many places around the periphery, whereas the surface instead has numerous rivers, lakes, and oceans. Impassable void is a pretty boring mechanic, since it offers no interactions at all -- no ships or swimmers or fliers or floaters can cross over it, and there's no way to tunnel through it or bridge over it or freeze it. The void also seems not to punctuate much of the interior of the map, so doesn't help to create separate regions and choke points nearly so much as surface water does. The main geography differences between shadow realm and caves are (1) that caves' completely impassable rock walls are sprinkled in the interior of large maps to separate regions and create chokes, rather than voids encroaching from all edges, (2) and that the shadow realm's only distinctive semi-passable terrain is mountains (which are completely un-terraformable, and mountainwalking is hard to come by), whereas caves have tunnellable dirt walls, lakes and rivers, and also magma that can be passed by a few units.
Suggestion #1. I think the Shadow Realm should have a lot more water. Not necessarily rivers like the other two layers, but a lot of pools and small lakes, including semi-long "finger" lakes that can help to create chokes. I think it could also be fine/interesting to include some lava pools (though it might not fit the color scheme, and so long as void continues to be lava-colored on the paper map, this could raise confusion.)
Suggestion #2. Void should somehow be semi-passable. As a first stab, I'd let floaters but not flyers enter the void (not flyers makes it distinctive, but also can be justified by absence of thick buoyant air in the voids). There should be a specific Void Passage ability, akin to Lava Walking, that a few other units have, e.g., Shadow Elf infused and touched and night guards, some/all shadow demons, draconian flyers, wyverns, dragons, floating undead, nightshade fairies, shadow stalkers, void serpents, horrors, cherubs, spy drones. Void Passage should be acquirable by a a variety of means, e.g., looted items, forged items, hero skills for self or for party, from a Shrine-like visit site, as a perk of rogue research, as a perk of some racial governance picks (e.g., it could be one of the mobility buffs goblin untoucha. Entering the void should be harmful to most units that don't have Void Passage, e.g., dealing 2 frost + 2 shock damage for each step taken in void. (Mechanically, this might mean making each void tile become a sort of visit site, which could also have the benefit of making an appropriately void-colored icon appear all over the void on the zoomed-out paper map, rather than jarring red lava.) Void should somehow be terraformable, e.g., perhaps with a spell that turns void into water (which then in turn could be bridged by a builder). If voids are made more passable and interactive, it could make sense to amp up the creation of pools of void in the interior of the map, which could help to segregate the map into regions and choke points.
Suggestion #3. Since the Shadow Realm has less interactive semi-passable terrain than other layers, Shadow Realm mountains should probably be a bit more interactive than surface mountains are. There could be a terraforming spell that lowers only shadow realm mountains (reflecting the ever-morphing nature of the Shadow Realm), and perhaps the corresponding spell to raise shadow realm lands to become mountains (though that might be abusable, especially versus AI). There could be a shadow-realm visit site that provides mountain walking (or shadow-mountain walking, if that's moddable), akin to the haste berries found on the other two layers. Alternatively/additionally a shadow realm visit site could provide *floating*, which would have the effect of providing mountain-walking, and forest- and swamp-walking, and if combined with suggestion #2 above would also give units a painful opportunity to cross voids. Several relevant units could be given mountain walking (or "shadow-mountain walking"), e.g., Draconian Chargers and Raptors, and Shadow Elf Exterminators and Archers. If mountains are made more passable, it might then make sense to amp up mountain generation in the RMG to help segregate the map more into regions and choke points.
Suggestion #4. Sites and lairs in the shadow realm could be better diversified. E.g., I see no reason why the Shadow Realm couldn't have Brigand Hideouts (with appropriate unit sets), Haunted Boneyards (vanilla unit sets should be close enough to fine since undead are already shadow walkers), Necromantic Circles (vanilla unit sets would probably again be close enough to fine), Dungeons (probably would need new unit sets and rewards), Libraries (existing unit sets would be close to fine, though may want to add the weed decoction enchantment to help living mages), Springs of Life (with new rewards and either new guardians or auto-casting shadow weed decoction), and Great Farms (would need new unit sets, or to auto-cast shadow-weed concoction, which seems fine enough for a place that's intentionally growing plants anyway). Incidentally the wiki claims the Shadow Realm won't have Wells of Souls, but it does, which seems fine.
Suggestion #5. The Shadow Realm is somewhat boring due to the lack of diversity of its inhabitants. It'll help if you can somehow get dwelling generation up to a reasonable level. I wonder if number of dwellings generated drops when available dwelling races is low, in which case adding more dwelling races (or even just carbon copies of existing races) would help produce more dwellings? One easy addition to the Shadow Realm would be Fairies, whose magical nature could easily justify Shadow Walking, or who could at least have a building to provide Shadow Weed decoction in their domain. I think it could be fine to have Giants in the Shadow Realm too, and to give them Shadow Walking. Of course, a Shadow Demon dwelling would be nice too! It would also be pretty straight-forward to create a Spider Dwelling, and spiders would be decent candidates to get Shadow Walking, and to dwell in the Shadow Realm (and other layers). Among existing full-fledged races, Halflings and Frostlings are probably the best candidates for inclusion on the shadow realm, since each is already somewhat magical in nature, and each already dislikes Subterranean so each is limited to a single layer, which would be a significant disadvantage. (Humans and High Elves are also limited to the surface, but humans don't seem thematically appropriate for either other layer, and High Elves probably need to be barred to maintain product differentiation from Shadow Elves.) In contrast, Shadow Elves and Draconians have a quite unfair advantage, in that they can happily dwell on all three layers, so it might make sense, for balance reasons, to cut a layer from each of them: e.g., making Shadow Elves dislike the sunny surface (so they'll just be Shadow Realm + Underground), and perhaps making Draconians dislike cave walls (so they'll be mostly surface and shadow realm).