I have two objects that have the same animations but different graphics.
Do I have to create two different AnimationSet and Link sections for each one of the objects, or can I share those sections and define different Animation sections?
I'm afraid your need two separate animsets if you're using different frames in animations.
However, instead of writing everything manually, you should create only the basic info in config and then programmatically build the 2 animsets in config at load time.
Something in the same spirit as what was proposed here to create animations from spritesheets without having to write manually the full blown config file.