I like the way you think, I got fun effects by allowing each critter to modify the dungeon in different ways. Putting two different critters in the same level got substantially different architecture than either alone.
I have wanted to write creatures that would modify the level, but haven't yet. What kind of approach did you choose and in what ways are they modifying levels?
I started off with wall modifiers because walls vs floor is the most meaningful terrain distinction for the player.
The function "koolaidman" looks at a 3 by 3 square of tiles and determines if changing the center tile could change the connectivity of the map. (this is because the koolaidman bursts through walls)
Rockworm larva move only orthogonaly and can burrow into walls that do not change connectivity. The creates a maze with walls a single tile thick.
### ###
.X. no #X. yes
### ###
Dwarf miners dig in straight lines turning 90 degrees whenever they find gold. When they collect enough gold they turn into dragons.
They occasionally create dwarf civilians.
Dwarf civilians remove exposed corners (unless it is next to a door)
###
.x#
..#
and place doors sometimes when they enter a room
#.#
#x#
..#
This combination creates a room and corridor layout.
Cave bison burst through walls that are only exposed on two opposite sides.
.#.
.X.
.##
this greatly increases connectivity and allows grass to spread so they can eat it.
Antelope clean up by removing walls that are exposed on three sides and do not change connectivity or wall connectivity. The finishes the transition from corridors to grassland.
There are also ants that carve a tunnel if
#
##
X
##
#
this creates a network of natural looking tunnels with plenty of short side tunnels.