Personally, I don't see any problem here; the idea that we can get closer to upstream and have less of a fork to maintain is great and has been a long-time goal of the project and ongoing effort by @techee, and this big PR isn't a whole bunch of new code we have to maintain, it actually greatly reduces the amount of code we have to maintain since it becomes upstream's code, and most of it doesn't get emitted in the final binary anyway. It seems like a big win for Geany.
Waiting for UCtags to create a proper library, which is a long way off, just causes volunteers to do loads of extra work in the meantime for no good reason.
That said, if this PR includes any files that are not used in any way, it makes no sense to include them, we should do like we do with Scintilla and leave out completely unused files, IMO.