I thought as much and so as mentioned above, before I did the activation I had moved those two files out of the GT86 mod folder before attempting to activate with GME - the warnings above have nothing to do with either of those files, they are about altering already -altered .dds and .mtx files having to do with the brakes.
Looking at where these altered files are put after activation it appears that in addition to the default location for the original versions of them in pCars\vehicles, or pCars\vehicles\upgrades, each mod installs its own unique version in MODS\carname\vehicles\ etc. So GME is not quite accurate in reporting the files have been modded, it's really that each mod is given its own unique copy so the activation should create no problems. Anyone know if this is the case?