This page lists some TODOs and known limitations of pyHanko.
Expand, polish and rigorously test the validation functionality. The test suite covers a variety of scenarios already, but the difference checker in particular is still far from perfect.
LTV validation was implemented ad-hoc, and likely does not fully adhere to the PAdES specification. This will require some effort to implement correctly. In the meantime, you should treat the result as a pyHanko-specific interpretation of the validity of the chain of trust based on the validation info present in the file, not as a final judgment on whether the signature complies with any particular PAdES profile.
The most lenient document modification policy (i.e. addition of comments and annotations) is not supported. Comments added to a signed PDF will therefore be considered “unsafe” changes, regardless of the policy set by the signer.
There is currently no support for signing and stamping PDF/A and PDF/UA files. That is to say, pyHanko treats these as any other PDF file and will produce output that may not comply with the provisions of these standards.
CLI support for signing files encrypted using PDF’s public-key encryption functionality is limited.