The check is just enforcing the legal interpretation of the rights holders, the check code itself doesn't matter legally. Just like how stripping some DRM doesn't mean you now own the copyright to the video.

That raises an interesting question: Is modification of the source that is used to produce the executable software necessarily modification of software from a DMCA perspective? Or does the circumvention have to involve influencing an extant binary in some way? The legal answer, in either direction, isn't obvious to me.

Especially since the GPL license does explicitly allow you to modify the source.