I know it is possible to use wrye bash to temporarily esmify the plugin you wish to use as a master, create the patch file which should be dependent on some other .esp, and then afterwards use wrye bash again to espify the original ''master'' so you can still upload your mod in the form of a .esp instead of .esm.
The problem I have with this is that any time I want to slightly tweak one of the patches, I first need to go through the process of esmifying and espifying the ''fake master'' again, and another issue is that it is more complex so other people will also have a harder time making their own patches.