Bitbucket 6 uses a 3-way diff in the pull request view, which hides some changes of the commits, if the same changes are already in the destination branch.
If you use the Compare diff view to watch the diff for the source and destination branch, you will see that the files actually got changed in the source branch. The same effect can be observed when you view the diff in PR for the individual commits.
Bitbucket 7 uses the 2-way diff also in the pull request view, like in the Compare diff view.
And Code Owners also uses this 2-way diff to calculate the Code Owners.
Background:
Release notes 6.10: Section: 2-way diff for pull requests
Release notes 7.0: Section: A modified behavior for diffs