The synergy is solid but I don't think it's a balance-breaking combo.
With a regular, single-species Lithoid empire, the advantage is a) that you get to colonize everywhere from day 1, b) your leaders live a bit longer (but the benefits are mostly eaten up by a starting age nerf), c) some niche early-game uses of the lithoid strategic resource traits. The point of colonizing everywhere is that you're actually growing pops on all those planets, so it more than makes up for the Lithoid growth penalty early on. Unless you are genocidal, single-species Lithoid has little going for it long-term, so you generally want to transition out of it by getting some biological species for better growth (requires bio ascension if Hive) and/or going for synth ascension.
Now compare to the situation of Lithoid necrophages + biological prepatents. You can still put your necrophage pops everywhere, sure, but you're not gaining growth from that because they don't actually grow. So for growth, you're still relying on the habitability of your non-necrophage species. The extra lifespan is also irrelevant. So the pros/cons of going Lithoid as a necrophage are less in both directions than they are for non-necrophages.
To add to this, Lithoids are less able to benefit from Bio-ascension, which is the natural Necrophage synergy.
Necrophage is mostly balanced around the difficulty of getting necro-pops. Unless you're a purging xenophobe/gestalt (in which case you have hefty diplomacy issues), the primary way is to build conversion buildings. At game start this might support 3 necrophytes a decade, but pretty soon at standard growth settings the 'limit by however many pops grown in last decade' limit will mean one per planet per decade.
Necrophyte conversion takes off at the technology Glandular Acclimation, which allows a flat 6 necrophytes a month- well above the rate of natural growth in the mid-game. Further, from this point on all necrophytes will adopt the primary template,
and the planet habitability of the planet they're on. In practice, if you get this tech by year 60, within 2-3 decades you'll have outweighed all natural Necrophage conversions you could have gotten on the colony beforehand.
The thing is, all of these converted pops will have 80% habitability on the planets they exist on, rendering over half of the Lithoid-necrophage's habitability buff utterly useless, and 100% useless if/when the player researches the Habitability techs for 20% habitability (useful for the prepatent workers) or embraces Bio-Ascension.
See, Glandular Acclimation is
also the tech for mastery of Bio-Ascension. Since a normal Necrophyte empire is already incentivized to bee-line the tech requirement for Bio-Ascension- and have the multiple species to make the most use of genetic fine-tuning- there's a synergy here... but Lithoids miss out.
Lithoids miss out because Lithoids can't take the Robust bio-ascension trait, which is by far the
best bio-ascension trait for necrophages. (They also can't take Rapid Breeders, but that's irrelevant outside of purifier runs.) Robust is not only 30% habitability (which takes non-Lithoids to 100% habitability on the worlds on which they are made, even without habitability techs), but a universal 5% job output buff, which Lithoids don't get but which does stack with the Necrophage's already existing selling point of 5% specialist/ruler output.
Tie these togethers, and early game your Lithoid-Necrophages do have a modest habitability buff when they are so few in number that they generally struggle to meet Ruler and a minority of your specialist jobs, but in the rest of the game your Lithoids will have no habitability advantage on other Lithoids,
and be permanently missing-out on a 5% buff to specialist and ruler jobs.
