Is Area 51 somehow like a per-site meta?
I haven't lost any reputation here, even though I have some down-voted questions here.
Yes. See the answer here: Why doesn't Area 51 have its own Meta?, which was posted by a former Stack Overflow employee:
According to Robert Cartaino, the Area 51 Discussion Zone is intended to serve as A51's per-site meta
so its reputation system is tied to the main Area 51 site, just like with regular Q&A sites and their metas.