Patchmanager patches have one patch file for all files that are going to be patched while prepatcher uses one patch-file for each file that's going to be patched in order to reduce the overhead that's caused by finding and applying a patch (which is done when the file loads so not spending too much time on that is vital).

However it should be trivial to write a tool which converts patchmanager-patches to prepatcher patches. (I might do so in the future).

Part of the point of prepatcher is that nothing special has to be done to enable/disable patches though so I don't see much of a reason not to simply distribute patches through openrepos since there's already a nice frontend for that (storeman).