The mod picker as it is works with RTC. The problem really is with RTC itself. It will only work out of the savegame folder and se4.exe that is in the Se4 directory that you specify in the RTC options. There is a way to make them work together. It seems very cumbersome, but using appropriatly named shotcuts it works quite well and is easy to get used to.
First of all you need to have a separate instance of RTC for each Version of Se4 (not each mod, jsut each Version). The easiest thing to do I have found is put a copy of the RTC programs in each Se4 directory. You can then have shortcuts to each on your desktop or a central location if you want.
Second you need to have separate instances of the mod picker for each Version. For the mod picker I think it has to be in the Se4 directory. I can't remember for sure but that works best even if it's not required.
Third, you have to delete the savegame folders from each mod folder. The reason for this will be explained in a bit.
Now when you are ready to play a mod PBW game you launch the mod picker for the appropriate Se4 Version. Then you select the mod you are using on the left side of the mod picker and hit the "Play SEIV button". This will rewrite the path file and launch the main Se4 startup screen. At this point hit quit game, but don't close the Mod picker. As long as you leave the mod picker running and don't start SE4 again with a different mod Version the path file remains as is. If you close the mod picker it changes it back to none.
Now launch the RTC for the appropriate Version and select your game. You can play it normally. The reason you have to delete all the Savegame folders in the various mod folders is that if you don't, RTC will lose track of the .plr file. RTC only uses the savegame folder in the Se4 directory you specify. It does not change to the mod folder because it doesn't look at the path file the way Se4 does. Without deleting the mod folder savegame folders you will be able to play your turn but Se4.exe will save the .plr file to the mod/savegame folder and RTC will look for it in the default savegame folder.
I don't think you are going to be able to rewrite the Mod picker to work with RTC better then this is without rewriting RTC which really isn't an option at this point.
However, I do have some ideas how you might write a standalone utiliity that works without the RTC or the mod picker and does what you are trying to do. If you want to email me I'd be happy to talk about it with you. I don't know how to code it but I know how the files are stored on the PBW server and I think it might work.
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Geoschmo