I've done attack chains (3 or 4 different attacks that play out in a sequence, for a platformer game).
I generally keep game-logical movements outside of Spine and in Spine, keep the character visually within the hitbox.
Spine Animation update rate (Update) is different from physics/collision update (FixedUpdate) and I like to avoid problems there.
I think you could go for some kind of root motion solution only for specific animations, if the movement is complex and has to be animated in Spine. Your hitbox can follow your character that way. I think the implementation depends on your game though.
Maybe other people have other ideas?