I haven't looked at the mod, but is it actually modular in the way that it adds a new folder to the modules folder? Look at the VD module for example.
The way it works is that every path in a modules folder that is exactly identical to a path in the main mod will override that path. For instance, if Assets\Art\Flags\England.dds exists in the main mod, Modules\FlagModule\Art\Flags\England.dds will override its content. This way you should be able to modify flags while keeping compatibility with the main mod.
The way it works is that every path in a modules folder that is exactly identical to a path in the main mod will override that path. For instance, if Assets\Art\Flags\England.dds exists in the main mod, Modules\FlagModule\Art\Flags\England.dds will override its content. This way you should be able to modify flags while keeping compatibility with the main mod.