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This can actually be solved by using "Calculate changelog against a specific branch" under the "the Additional Behaviours" options under SCM.
This option will let you pick the branch you want to calculate the changelog from.
You also mention PR against different target branch. I think this should also be possible if you use the ghprbTargetBranch env variable as the branch to calculate the changeset from.
That being said I do not know if that field supports environment variables. Using a static branch name such as "master" should work on the latest version.