I think it partially started out with Dench being cast - and, ironically, with the decision this should not be a reboot for Brosnan. So Dench‘s M was the new hand on deck and there had to be ‘issues’ between them. Although everything except Q was new, the Lego headquarters, the interiors. It wouldn’t have been a big thing if had they called this a reboot.
When Craig arrived in his reboot the writers once again went back to their default position of ‘issues’ between M and Bond, this time she supposedly doubting him. Actually, wouldn’t it have been a stronger dynamic if she hadn’t had any doubts regarding Bond? After all, he didn’t arrive in the 00-section because he was employee of the month three times in a row. Let others doubt Bond and blow the top of their heads. M’s the one who sent him and, whoever M is, they will have had their reasons.
Craig’s tenure turned out vastly different from what one may have expected after the last frames of CASINO ROYALE. Some of it was no doubt due to considerations about how genre cinema was received during these years - a version of the series picking up on current trends and playing them with an 007 theme like MOONRAKER. As you said, the success is what justifies these decisions, up to a point.
Since these films have evolved into their own series within the series it’s hard to imagine Craig’s successor will not star in his own reboot again. Maybe that reboot will then look for other themes, will keep its distance from the person of Bond for a time and instead look for its own way of telling a fantasy spy romp. We only can speculate - but we shall see.