"as far as I know none of the propositions made in Anarki can be found in the official versions"
There are a few bug fixes that appeared first in Anarki, were brought up on the forums, and ended up being added to arc1 or arc2. But you're right, I don't believe PG pulls changes from the repo directly.
I'm no lawyer and I haven't read the artistic license very closely, but Anarki's under the same license as the original codebase, so I'm pretty sure there shouldn't be a problem...