Your assumption would require a complete shift in his entire philosophy...for what reason? What, after 5+ years of handing over "GM duties" to pursue more high scale business-driven responsibilities, he all of a sudden wants to go back to calling the shots on which waiver-wire pickups we're making? Really?
Again, why is Ben Cherington still here then? He was the GM of the Boston Red Sox and can easily leave at any moment for a similar position...and yet I am to believe that he is willfully spending years here in which he (by your own claim) really has no decision making power? A guy like Ben Cherington isn't sticking around here so that he can fetch Shapiro's coffee in the morning...and AGAIN: Cherington is technically BELOW Atkins, so if Atkins is really just an "assistant GM" under Emperor Shapiro, then where does that place Cherington? Cherington is in play for PRESIDENT positions at other organizations LOL.
This front office is filled with high-end executives with 10+ years of BASEBALL experience. Guys like that don't sit around and play "yes man" for a job title; they want to stamp their own name on whatever the team is doing, and all of these guys have the clout and resume to go do that elsewhere if they aren't doing it here. Your Masai Ujiri/Bobby Webster example isn't even remotely comparable. Bobby Webster came to the Raptors from the NBA front office wherein he oversaw cap-limit planning: he had virtually no actual basketball operations background so OF COURSE he is only a "GM" in title as he is in fact a "business" guy who hadn't even worked for any other team prior. The Blue Jays in comparison have at minimum three guys (Cherington, Atkins, LaCava) who are qualified to act as GM, and have either held the position or been in STRONG consideration previously. Atkins, by the way, interviewed with more than one other team prior to being hired as GM here. He also has 10+ years working in basically every level of baseball operations, comparing him to Bobby Webster is a joke.