While the Kraft's have given Belichick carte blanche as they should have, they are also very unsentimental people. They are not given really to sticking it out with Brady if the braintrust (correctly) thinks it will hold them back from rebuilding, nor do they risk offending the power structures in the NFL that will put a bullseye on the team.
This is why I believe they would never go for a set-up like the one above.
If Bill B. is really thinking about a future as HC for his son, he could make it mighty uncomfortable for the Krafts by declaring himself GM and installing his son.
That would be a dilemma. But Bill also risks damaging his legacy if he does that.