I haven't tested the last files you sent me, probably tomorrow, but I have one question: You are actually saying that IWTE is required to alter the paths for each submod? This would mean that even if you were the one to do this, it would only work for TATW and for no other mod. If this is the case, to play custom settlements in every possible mod and submod (that has custom settlements, that is) one would have to be directed to you to ask for the change.
Not very handy, is it? A better, if difficult, solution would be to make IWTE work for Linux. WINE doesn't seem to be able to run it, so my guess as with all modding tools around is that a language needs to be downloaded and installed. Do you happen to know if this would be the case with IWTE?