I don't know how well know this is, heck it might be common knowledge, but over spending the better part of a year trying to get the Linux versions of the IE games and modding to work, I found an interaction with wine environment and weidu.
In the time I've been messing around with it, I learned that you can't run weidu in wine. It just won't start. Usually. While weidu exes don't run, self extracting archives that install the files and launch weidu for you DO. So say, SCS and its executable will run in wine. But a zipped file that needs to be extracted manually with the weidu exe in it won't. This let me move the linux version of BGEE into a wine environment, run the installers for mods, and then move the game back to its home folder. I've played about 4 hours into BGEE with CDTweaks and SCS installed and everything seems to be working correctly so far. I know nothing of programming, so I can't even speculate on why this makes any kind of difference, but this works.