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I think that is "by design" of the git plugin.
A GitHub pull request is a request to merge something, and the GitHub Pull Request plugin needs a destination for that merge. I assume that destination is set in the git plugin advanced options section.
I think you'll also need to add a post-build step to use the Git publisher to push the merged changes back to the destination branch. If you don't add that post-build step, then the git plugin will perform the merge to the base branch each time, and report all the differences each time (I think). At least, that is how my experiments have worked when using the git plugin to merge changes from multiple git branches (without the GitHub pull request plugin).