Most programs that read MTL files have their own quirks just as they do for OBJ files.

The best thing to do is to remove any texture paths (leaving only the filename) and put the textures themselves in the same directory as the OBJ and MTL.

Make sure any file references in the OBJ and MTL match the letter case correctly to avoid problems on Macs.

Don't worry to much about the material settings, they pretty much need redoing for any given renderer.
Any transparency must be done in the target program as that information isn't part of the MTL spec.