How to update build status for PR merge commit
Assuming the PR is mergeable, you can fetch the reference refs/pull/NUM/merge, where NUM is the PR number, which should contain a merge of the branch in the PR and the base branch. That should be available either immediately as the PR is opened or shortly thereafter.
Once you've tested that, you can just create another status if you want. It may be useful to create an in-progress status first in order to prevent people from merging without running both sets of tests first.