The Easy nine said:Does this mean I'll have to manually install it?
modmerge assumes a lot of stuff. If you change the base stuff, those assumptions are not longer valid. So it probably won't work on anything that is not Native. Simple as that.
you can use modmerge as a tutorial/recipe on how to integrate the code changes into your mod, and do it manually. Just follow the steps from the package. The more changes your base module has, the more coding work (adapt the changes) you will have to do yourself.