Then why not just appoint YOURSELF as GM and be done with it ? Like I said, if I was Cherington, that's exactly what I would do, especially since he's the one who will ultimately be left holding the bag when Valentine flames out spectacularly in 2 or 3 years.
I think you are hung up on the titles of GM vs President of Baseball Operations. Its evolved recently, but essentially POBO is the de facto owner. Ie who was the GM when Steinbrenner was running the Yankees? Didn't matter, George was THE BOSS. In the current Sox case, John Henry is the majority owner and a squishy ball of goo, so he defers his power as do the other owners to Larry. But Larry doesn't want to deal with day-to-day stuff of being a GM so he hires a younger guy to do it. Your issue is the same as Theo's problem when he quit this year and when he walked out years ago in a monkey suit, namely the GM isn't in charge. Larry Lucchino is the boss of the Red Sox and it really doesn't matter if Ben Cherington is the GM or the assistant GM.
Incidentally, Theo begrudgingly realized this and that's why he's POBO in Chicago and not GM.
Only negative thing about the manager hiring process is that it took way too long and the Cherington v Lucchino differences became obvious publicly. That's Lucchino's fault because he's ultimately in charge, and arguably he did that on purpose to put Cherington in his place immediately. You'd think that'd be unnecessary if Cherington was witness to all of the Theo-Larry dynamics over Theo's GM tenure. So I'd speculate Larry has an autocratic style that makes him need to publicly & private establish his power. This isn't news, but its a bit off-putting that he needs to publicly demasculate his employees.
Maybe Larry also thinks this helps their dealings with others in that any trade partners know that the GM's word is ok but they'll need Lucchino's signoff before they know they have a deal (sounds bad, but for example would anyone be comfortable making a trade with the Cubs today unless they KNEW it had Theo Epstein's support)?