The current boss situation seriously skews gate composition and leads to a lot of repeated playing of the same few levels.
In an ideal world, this would probably be solved by a greater variety of bosses--like, say, 26 new ones (one per theme per tier). At a minimum, I would like to see the existing bosses reduced in frequency, so that at least the slime and construct themes won't be taking up >50% of stratum 4, even if the slack is just taken up with perfectly ordinary levels.
But a middle road approach would be to create a large number of lightweight "boss-like" encounters as efficiently as possible. To that end, I propose: mini-bosses. Mini-bosses can appear randomly on the last level of any non-boss stratum, and are not necessarily the only level appearing at that depth. In order to be able to fill in all strata and themes easily, mini-bosses are constructed algorithmically from existing content, requiring minimal individual work.
To construct a mini-boss:
1. Select a monster appropriate to the theme, but that would normally appear 1 stratum deeper.
2. Make it about double normal size in every dimension (just a stretch, no new assets required). This affects collision size, hitbox, and the area hit by the monster's attacks.
3. Make it move and attack about 25% faster than normal.
4. Give it around twenty times its normal health.
5. Give it boss resistances (reduced status duration and resistance to interrupts or whatever you normally do).
Then drop the boss into one of a small number of specially crafted mini-boss arenas (probably 2-3 designs, plus status variations where only the colors and floor traps are different). These each include ~4 spawning tiles that endlessly create monsters that might normally appear with the monster type selected for the mini-boss, but which do not drop crowns, heat, or materials (just like the supporting monsters in existing boss fights). The supporting monsters are never healers, but just about anything else should work fine (even turrets, if the arenas are constructed to give them reasonable coverage).
Mini-bosses could drop either a new type of token (common to all mini-bosses), or sparks appropriate to the level's theme. More tokens are dropped on deeper strata (equal to the stratum number seems like it might work fine). After the mini-boss room, there are treasure chests and minerals, similar to a full boss.
Perhaps not every monster type would work well as a mini-boss, but most should.
Ta-da! You now have bosses for every possible stratum and theme.
A giant/harder version of an existing mob?
Um... Lichen Colonies? Alpha Wolvers?
The random appearance of higher-tier monsters in place of a regular monster of the same type in a few of the levels?
Plus quite a few of the monsters are miniboss-y in some ways already... Trojans, Phantoms, (Grimalkin are more like a puzzle boss, not sure if they count) and amongst the removed monsters there is the tortoise thing (though witness statements suggest that it's impossible to do him on your own) and a giant green jelly (which apparently also had tiny helper spawns). Putting them through this sort of treatment might not work so well.
It does seem like your algorithm might end up as an invitation to maximum monster redundancy... the rest of your suggestion varies from "interesting" to "you might need to put a little more thought into this"... I dunno anything about rendering but it sounds as though the double-sized monsters might not look so good.