If I say "Please don't use this software if you make more than $100k/year" I haven't added an additional clause, just communicated a desire. I'm as annoyed by parallel's citation nag (particularly since I don't plan on ever publishing a scientific paper), but it does not impose extra requirements.
I think I agree with you: if you put in requests that have no mandate or attachment to "or this changes your rights under the license", there's no issue.
But I was responding to the comment upthread "You can add any message you want into your GPL program". If you add a message that says a user of the software must do something / must agree to additional terms / etc, that additional text is not compatible with the GPL. I'm not a lawyer, so I have no idea whether the result would be that the restriction doesn't count and the software is GPL'd, or that the software isn't viably GPL'd because the GPL+clause isn't a valid license for somebody to use.
