I'm using pdftk 2.02 under Windows successfully except that permissions do not come out as expected. Even with
pdftk.exe input.pdf cat output output.pdf allow AllFeatures owner_pw test
the resulting PDF shows that "assembly" and "page exctraction" are not allowed. Specifically mentioning "allow Assembly" does not change this either.
What's wrong?
Turns out the problem does not really exist. When using Adobe Reader to check permissions, it will always show that assembly and page extraction are not allowed. While this seems to suggest that the lack of permissions comes from the file, it is actually because the Reader won't allow it. Opening the same file in the Pro version does show the permissions exactly as desired.