We allow generating Pull Requests from a forked repo. It currently assumes a lot and I'm bumping against the limitations now. It assumes that the current branch is the "compare" on the current repo. That seems fine to keep. The problem is that we can't change the base, which is hard-coded to be the parent repo (that the fork came off of) and that repo's default branch.
At the very least we should allow selecting the base branch. Ideally we'd also allow changing the base repo to any repo in the network of forks.