Generally speaking, animation is a cosmetic layer. The CharacterMovement component uses the capsule. As for why the out-of-box functionality is what it is, my guess is that Unreal tries to keep things pretty general so that they’re easy to use in projects that have wildly different demands of the engine. Depending on the needs of your project, you might be better off building some functionality from the ground up rather than trying to work with the inherited behaviors. Again, it depends exactly what you need for your project.
As for the animation stuff, I don’t think retargeting an animation from another skeleton to the Unreal Mannequin would have any effect on the functionality of Crouch/Uncrouch. Is there a particular reason you wouldn’t want to do a trace check before executing Uncrouch?
You may also be having issues with collision settings. Does your capsule stop colliding with certain objects after crouching or uncrouching that it collided with before? Are you trying to perform collisions with the mesh and not the capsule?