I've done a number of playthroughs over the years, both vanilla and heavily modded, and I've been kicking myself for not noticing this. I've always attributed it to Rockstar's awful RDO updates breaking singleplayer. No wonder I could never find any flamingos, badgers, or even chickens.
Basing this off the chicken run test posted earlier (loading into Valentine and seeing how many chickens appear near the pens), here's my current list of mods:
Timescale
Extended Player Animations
NPC Aiming Animations
Improvements in Blood
Lost and Found Scout Jacket
Flo
A.E.M
1899 Firearms
Natural Dirt
Online Content Unlocker
GunFX
TKoul's GameConfig
[A whole bunch of .asi mods]
FirearmCosmetics WILL break the game. I've been testing with/without it and it consistently deletes both chickens and tram passengers. 1899 Firearms works without it, but I'll update this post as I start a new playthrough and if I notice anything breaking.
Thanks for all the work testing this issue, this is one of the most insidious mod-related issues I've ever seen.
Edit: Here's WickedHorseMan's Firearm Cosmetics compressed to BC3 / DXT5 Linear. Wish I could compress to higher res but I can't get RDR2 Texture Toolkit to work past DXT5 linear.
Works on my machine, TPs around the map saw me chickens and trams.
Unzip, stream folder goes into lml\WickedHorseMan\Textures\FirearmCosmetics. Overwrite all.
https://mega.nz/file/FGBUTLrB#klA-bJjOPHKTvbvNlxC4FaHl6yL7ZZrf7cV4fEweZ8o