The way I see it, plenty of mods include fixes as part of the mod. At some point USKP may pick up the actual fixes for what is literally broken in vanilla, and any mod worth it's salt should be carrying forward fixes made in USKP anyway, as long as the mod doesn't need to change explicit things fixed by USKP in order to provide the desired functionality. If/When the USKP team merges the Vanilla fixes from the mod in question, it's obviously the point to drop those fixes from the mod as long as it doesn't mean dropping anything that the mod alters and thus depends on, in which case you leave it because at that point the mod is "carrying forward" those fixes that are a part of the USKP.
That's just my opinion on the matter, but I've seen it play out that way with plenty of mods already.
I would say, do whatever makes supporting the mod easiest Kryptopyr and if that means packaging in a few fixes with the mod then so be it. :)