Nowhere does RMS say that, oh, if the user modified the program, it's okay to limit their freedom to run it in some ways, as long as it's via a license blessed by the GNU project and the FSF, the ultimate arbiters of what is free who can change their minds at any time.
However, in this article, RMS is cheerfully recommending Affero:
There is a lengthy article by RMS "Why programs must not limit the freedom to run them".
https://www.gnu.org/philosophy/programs-must-not-limit-freed...