I think we need to remember the Lore as much as the rules.
Yes, those mechs that need the stock DHS in engines to do anything are going to be in a rough spot, relatively. But so is everything else. What they will still have is versatility. The flip side here is the various Jack of All Trade mechs that are suddenly more useful too, despite being all but useless in base TT games.
And hey, sometimes dealing with an overheat shut down to get an alpha strike is worth it for these other mechs too.
But in the novels and other fiction? Even those heat neutral clan mechs don't run heat neutral. Pilots RARELY alpha strike in any mech, EVER (Heck, remember Thunder Rift? They mention the LOCUST runs hot! that's physically impossible by TT rules!). IMHO, those mechs will finally work more as designed, and if anything are left with some redundancy.
Heck, this game made the SHADOWHAWK useful. That mech is GARBAGE in the TT game compared to most of the other stock builds out there. Here? It's worth it. So I have faith, and am not bothered by the energy thing.
Also, there's at least one item in the game that reduces heat build up on energy weapons by 15%, it does weigh 3 tons, but it's possible a '0' tonnage one might exist for some clan mechs to make up for things too. So yeah, there's ways out there.