you probably figured it out already, but the animation only needs skeleton to work. you can associate any skinned mesh with it later non-destructively.
Are you working in Maya? If so, you can leave the triangulation to the fbx export (turn on "triangulation" in the export dialogue) and leave your source model in quads. I believe it uses Maya's triangulation method, which is to create the shortest edge possible to create triangles. Anyone exporting the skinned model as an…
The fact that animators and TAs prefer to work on quad models doesn't prevent the ingame asset to be exported with known, locked-in triangle edges. The models only get baked and exported once ... In practice you'd have to bring this up to whoever is in charge of the tech in your project, and not bulge from there. Otherwise…
I did not :# How can you make sure that the animated version of this model has the same exact triangulation? I'm assuming most riggers and animators preffer to work with quad models. But you're right, this is most likely the issue!