I don’t know for sure, but sometimes CH wants layers inside a group, even if only one thing in the group. E.g. all your “Bottoms” are direct layers (no group) and so cannot have the crown (independence) turned on. Because the are no independent, the “dependence group” as I call it is the merge of all the things (shown or hidden). As a result, you notice the yellow bounding box is not following the contour of the object? I am wondering if it is getting confused for some reason, with different origin positions based on centroids of the artwork.
Bottom line - a suggestion to try (with no idea why you should need to do this but just suggesting things) is to put a group around each child of Bottoms. E.g. turn ”Body BD Shorts Brown” into “+Body BD Shorts Brown” group around “Body BD Shorts Brown”. Then you should get the children of Bottoms to be independent. Maybe try a few and see if that makes a difference. You can then adjust the origin marker of those layers if necessary.
But I am not sure why what you have is not working - just suggesting possible lines of investigation. I never like the yellow outline being like you show - it messes up warping. I think the multiple optional layers (including hidden ones) is too confusing - using the crowns for independence I think will reduce the scope and get the contours right....
Oh, in the rigging panel, did you try just dragging things back into position By the way? Worth a shot!