Force duplication of sub-resource to fix make sub-resources unique on MeshInstance

[gururise]

Force duplication of sub-resources on "make sub-resources unique". This fixes #33823

Attached GIF showing this fix works:

[gururise]

FYI, this might be a good cherry pick for 3.1.2 as the bug also affected v3.1.1

[Xrayez]

This affects all type of resources though, the question is whether Make Unique should make sub-resources unique as well by default, or should be there another option for that. I think some cases may have cyclic references which could lead to crashes if resources reference each other (because of recursive nature of duplicate(deep=true).

If resources are all built-in, it may be safe to assume that making all sub-resources unique won't crash anything, but I'm not sure what's the proper way of checking that (likely built-in resources have empty resource_path).

[gururise]

@Xrayez Agreed. This is probably not the right way to fix the issue.