Will animation file size be different if mesh data is included in the .fbx?

Assuming two scenarios, using 3ds max
Main character is exported as a .fbx file, with no animation data. Animations are loaded from other fbx files.

  1. .fbx file is exported with skeleton only, file is otherwise empty.
  2. .fbx file is exported with other data in the scene, reference planes, the mesh the fbx animations will eventually drive in the main file, etc.

Will the final project file be the same size? or will the one made from “optimized” fbx files be smaller?

It does not matter if you include the animation data or not in a mesh. A FBX file with a mesh and animation data should have the same size if not a lower size than TWO FBX files of which one contains mesh data and the other one only animation data. Of-course to play it save it is always smart to keep your rigged mesh and animation data in separate files. Only the files that are used in the project will eventually determine the size of your final build. I for instance have 1 file containing my rigged mesh and 1 or multiple files containing all the animation data in separate clips.

I hope this answers your question.