I dunno. Things look pretty different between "All Good Things..." and ST: First Contact, and that's only a few years difference too.
As for what Gene thought: He wanted TMP to invalidate TOS and be its own thing, because he no longer owned TOS. Then when he was executive producer of TNG, he wanted that show to invalidate TOS and every TOS film that wasn't TMP, and be its own thing too, because he didn't own any of those things either. Except when he no longer had creative control, the people in charge ignored his intent and just treated it all as the same continuity, which everyone does to this day.