I am confused on the proper way to manually merge a pull request, and to understand why there are different suggestions regarding it.
Suppose the simplest situation: one
git fetch origin
git checkout -b feature origin/feature
git merge master
git checkout master
git merge --no-ff feature
git push origin master
For your point 2, it doesn't say to merge the story into master because that's not what the OP wants to do.
Regarding your question. Let's assume we have this:
master *---*----*----* \ ---*----* feature
If you merge master into feature, that will bring all the changes made into master to your feature branch. the feature branch wil contain the atest changes from master + the changes in the feature:
master *---*----*----* \ \ ---*----*--* feature
master will thus still point to the same commit as before, but feature will point to a new commit, which has all the changes for both branches.
So you still need to merge back the changes from the feature to master. That's a very simple operation now, since master is an ancestor of feature. So mergining is a simple fast-forward:
*---*----*----* \ \ ---*----*--* feature master
I much prefer keeping a linear history, and thus rebasing the feature branch on master before merging it into master. But your mileage may vary.