I have a set of documentation for my company\'s API, based on the excellent Slate framework from TripIt. Per instructions, I forked their repo and proceeded to customize it.
It is unfortunate that GitHub does not provide a way to configure the default PR target repo.
If you can delete (or get the owner to delete) the original repo A from which B was forked, then that will do the trick.
If it is not possible/agreeable to delete A, but the owner of A is willing to do the following, then the fork link gets broken, on GitHub Enterprise at least:
After doing this, repo B (which was originally forked from A) will default to opening PRs against itself, rather than A.
Note: if A itself was forked from something further back in the history, then unfortunately it seems that B starts defaulting to opening PRs against that repo once A has gone. The only solution would be to apply the above to all repos upstream in the fork tree :(