I have not used a AnimationTrees, but could you just show/hide the parts of the 2D character using another AnimationPlayer, like something called VisibilityAnimationPlayer
for example. Then VisibilityAnimationPlayer
could have animations for showing/hiding each part, which you could call either from script or potentially from the AnimationTree using a event/function callback.
I"m not 100% sure it would work, but it might be a way to work around the issue.