If you add a module that edits the spnpccharacters.xml and activate it. It will add the stuff you edited but not overwrite it.
For example, if you create new equipment for certain Native units, instead of overwriting it you will add it to the spawnpool. Making them use half from native and half from you.
I'm also looking for a solution. Editing the original .xml is not ideal. Since it breaks with every update.