I think there is a slight bug when transmuting Enscape proxies. Even if transmutr is set to produce relative texture paths the source flag in the material xml is still set to absolute (while the actual path has correct relative formatting):
Ok, so after some further testing I realized that I was completely wrong.
By changing the xml to:
the material xml becomes semantically invalid (from enscapes point of view) and Enscape discards the xml and use the plain Sketchup material which contains the texture. Thus, it was an illusion, it never really worked!.