Fix some corner cases in difference analysis

[MatthiasValvekens]

Description of the changes

Bugfixes to difference analysis:

• Adding XMP document metadata where there previously was none -> allowed
• Allow /Extensions and /MarkInfo to be indirect in the document root (but their contents still have to be direct)

Checklist

Please go over this checklist to increase the chances of your PR being worked on in a timely manner. Deviations are allowed with proper justification (see previous section).

• [x] I have read the project's CoC and contribution guidelines.
• [x] I understand and agree to the terms in the Developer Certificate of Origin as applied to this contribution.
• [x] All new code in this PR has full test coverage.

For bug fixes (delete if not applicable)

• [x] My changes do not affect any public API or CLI semantics.
• [x] My PR adds regression tests (i.e. tests that fail if the bug fix is not applied).
• [x] All new code in this PR has full test coverage.

Additional comments

Result of PDF TWG mailing list discussion.