You are getting river milkfishes or oceanic milkfishes?
It's ocean ones, sorry I don't have the save when they're on map, but my fort is very young, have 40 dwarves, not too much stone, and is regularly cleaned with dfhack, so I'm pretty sure it was them. I'll put those numbers back and upload save when next wave of them arrives.
Do undead share those settings with normal animals? Because 100-150

undead tunas could literally siege you. However I haven't seen any fine embark with evil ocean in last 20 worlds I generated.
+ Inedible body parts and seeds will no longer rot.
Does it mean we'll need to haul them to trash compactors once again? Or we always had and now they just remain the same while we're doing it? (I hadn't paid much attention to refuse piles)
+ Made large trainable creatures inedible and require a combination of meat consumption, alcohol consumtion, water and sleep depending on the creature.
We now can't butcher elephants?

+ Elephants & poisonous pets require booze
Poisonous pets? Which are these?
+ Dragons & hydras require meat, booze and sleep

I really like this one.
Reason being the high amount of wildlife a fort can assimilate and set loose on sieges with little thought, making sieges actually damage less then random unlucky death to wildlife.
You know, player can wall fort off and thus make siege damage only fps. And I although your deer are deadly (hate those bastards) in the wild I doubt they'll cause much casualties to well armed and grouped squad of goblins.
Also, I'd like to upgrade my current save, which raw files have you altered?