Here’s my thought process:

- the GNU Parallel author(s) want/wants people to use and contribute to it.

- they think that most users are academics who write papers and that potential users will find the project after reading the citation, which may or may not be true

- they include a nagware message that “reminds” users to cite the software

- despite the message being controversial and being the subject of the #1 comment in an otherwise unrelated HN thread about the software in general, an FAQ is written to back up the existence of this message

This brings me to the question of whether the inclusion of this message acts more as a deterrent to potential contributors and users. I agree with the motivation, but the means feels petty and undercuts the original goal.