Hi Markus,
if you merge such PRs into a "bucket branch" (which isn't synced with the main development branch by definition) the consequences would be even worse: You will have a bucket branch with changes from _many_ pull requests which diverged from the main development branch for quite some time. This would be even more difficult to merge later on.
The (only?) advantage of keeping PRs open for such changes would be that you get rather small changes which are more likely to don't result in conflicts and you can even switch target branches for the PRs directly in GitHub if you decide to merge it somewhere else (like directly to "master").
However, how to handle changes which shouldn't go into the main development branch immediately is a matter for taste.
Another alternative would be to use feature branches for such changes. So we could for example create a branch "deprecate-at-context" and merge a corresponding PR into this branch. This way we get the advantage of rather small changes per branche and we don't keep PRs open too long.
Just my 2 cents. ;-)
Christian