To whom it may concern,
It was requested by Stuart Mumford and I also find this option convenient in my other projects, so as an experiment, I have enable "update branch" option for pull requests on astropy repository. I think "rebase" is preferred. Please see screenshot below.
Note: If you do not like it or do not trust it, you do not have to use it.
If you do end up using it and find problem, please report back. We can always disable if it does not work for our workflows in the astropy core lib.

Thank you,
Pey-Lian