FYI, I've fixed plist generation wrt new manpage path, see r531317.
And another problem is that the build system has optional dependencies which are not listed in the port, namely asciidoc. It's absence when package is built leads to missing manpages, and it's optional presence on user host leads to inconsistent package contents.
Also I'd advice against fully dynamic plist as it allows problems like this one to be missed. You can generate plist dynamically for python part only, leaving binaries and manpages in static plist.
A commit references this bug:
Date: Fri Apr 10 15:47:03 UTC 2020
New revision: 531325
net/ntpsec: Fix build; Add missing dependencies asciidoc and mDNSResponder; Correct LICENSE
PR: 245503 245502
Reported by: amdmi3 email@example.com
Fix committed, thanks!