The moders are silent about this indeed, maybe because it is not possible to import banners and flags for id's that are not set by EA to have these graphics or maybe they don't want to share it because... now mods are monetized, idk. But it is a bit pathetic if it is the last reason...
You can try this trick, but i don't know if it works, never tried it myself and if it works it is only for one team. Or you have to replace the graphics before launching the game each time you play with another of your created teams:
In your squadfile or career (if you have an ongoing career) db, in the teams table, columns "isbannerenable", "haslargeflag" and "skinnyflag" set the value form 0 to 1 for the team you created.
Then you will have banners and flags but the banners will be blank, all white and the flags will just be giant corner flags or with some generic 21 (why 21?) marking.
I think you can change it by replacing the banner0 and flag0 graphics with fifa editor tool. These are the files of the blank banners and giant corner flags. As said it is just a trick, not like having the graphics assigned to a proper id but i can't see any other way to achieve it.