A, because B won’t do what you think it will do. If your .gltf file contains animations, they all get imported. Saving some of them only makes those animations editable in the AnimationPlayer. They will all show up.
If you want to cherry-pick animations to appear for memory reasons, you need to load it up in Blender and delete the animations you don’t want to import.
So for B, I would have a list of animations for that character as files and then Import my character .gltf (with only skeleton and mesh, no animations). I then create animationPlayer and pick and choose animation files from animation library.
Does it make any difference? for example A would be 3 characters each with all animations shown in their animationPlayer vs. B with 3 characters with fewer animations shown.