Benintendi, Betts and Devers were identified as franchise caliber talent - and there were job openings - so there you go. Margot (for instance) was blocked and lacked the upside - so he became trade fodder. And remember, considering how crappy the life of a minor leaguer is (scandalously low pay in particular), this is for the best.
Dombrowski has done a great job here - been very aggressive with the guys he believes in and have moved other guys. One of the big failings of the past administration was not necessarily making those decisions so the organization had some direction. As I've noted before - while every team wants to be a scouting and development machine (and I desire that for the Red Sox of course), we are not the Oakland A's, and the franchise should not act like they are (and fortunately they are not), and the fans pay way too much money for that sort of rationalization. (whether that be rationalizing not signing a premium asset, or mainpulating service time with a guy who obviously should be here)
Now, the Red Sox have largely done the right thing organizationally and have benefitted from a rather amazing set of prospect graduations. The challenge is replacing them, but that would have been true no matter who the GM was.