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Reviewing this question, we found the following:
a) A forked repository will show the upstream repository's default branch as the base branch for any pull request generated through the interface
b) A command line tool like cli (https://github.com/cli/cli) can be used to generate a pull request while specifying both the base repository and the base branch, so that pull request generation doesn't default to the upstream repository.
We also want to check if we can generate a pull request from a repository that is not a fork. (We would also need to check if we can pull in changes from the upstream into the non-fork). That can be a separate GitHub issue if need be.
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