Really good Hubert, mods will be easier to handle in such a way.
Just a question, would it be possible to select and play 2 gfx Mods at same time?
Eg: Highres counters + IronX flags
Yes, the way it will work is it will load mods in the listed order shown in the MOD selection screen. It will load the first mod selected, and then the second mod selected and so on. If there are graphics in the second mod that are also modded in the first mod, the second mod will overwrite the duplicates in the first mod.
For example, in IronX's mod he has edited the flags, but changed the flags back to the non swastika symbols. However in his real flags mod, if this is also loaded, then the historical flags will overwrite the flags in the first mod.
Hopefully this makes sense, and while there is currently no way to list the mods in a specific order in the mods screen, the mod screen does list them by default alphabetically, so as long as you rename the mod folders alphabetically in an order that you prefer, it should work as needed.