Hey there,
The Mutable Cloth plugin is an extrapolation of all of the cloth code into its own plugin so that we can continue to improve cloth functions and broader support for Mutable. It’s the same functionality, and that warning was added to help indicate that you might be using some of the functionality. Mutable cloth right now only works with SkeletalMesh cloth, and it handles when you remove mesh sections if you are doing any clipping. If you are seeing your cloth work correctly afterwards, that is good, but what you want to look out for is that any mesh-modified cloth is working correctly.
Dustin