Hahaha I was JUST chatting with Liquid Smoke about this! I think this is not just a feature, or something that could be done, but is now out of necessity.
This would not only eliminate conflicts, it would allow skinners to put their information needed for the skin in their own skin folder in say a skin.ini file. This would eliminate someone having to muddle through adding stuff to the RR.ini whenever a skin is installed.
Many skins, including mine have sections to add to the rr.ini that the end user has to do. If it's 20 lines long, that means to do it properly they have to look at each of those lines and make sure they are not already in the rr.ini in the first place, which is not an easy task with the non-standard format of the rr.ini file.
This would be a major advancement, and I for one am hoping and praying this comes to be.