I've got several versions of the same avatar which use the same body model (they have different outfits), and use a number of constraints for body shaping/deform (twist bones, muscles, shaping, etc). So to make my life easy, I put a bunch of VRC Rotation Constraints in a prefab, just like I do with my physbone settings.
Unlike physbones though, this is a source of great frustration.
The #1 issue is going in and out of playmode seems to randomly deactivate one or more of the constraints - which one seems to be different for each avatar, but it's 100% reproducible for a given avatar.
Another issue I noticed was trying to apply or revert prefab settings - a reproducible case is to have two rotation constraints on a single GameObject in a prefab, activate both, then try to apply or revert any setting for one of the constraints while watching the other one - you'll note it has some settings change unintentionally. While avoidable, it's still probably not desired behavior.
If I unpack the prefab, everything works fine and the settings never get changed, but then it's much harder to share settings across avatars.