I don't see a problem with a second pull request that originates from a different branch. The question is if these changes interfere in any way. This could result in a conflict depending on which request is processed first.

The master branch in Git is technically nothing special. It's special purpose is just a convention.

I'd go along something like this:

git checkout master
git branch feature_x
git reset --hard upstream/master
git pull upstream master
git checkout feature_x
git rebase master
# edit feature x
git add .
git commit
git push origin feature_x
# create pull request
[download]

EDIT: changed personal alias "co" to "checkout"