I agree with Ron. Boone should've never been hired in the first place. It's analytics on steroids with no feel for the actual players or the game.
The problem I have with analytics exactly what you touched on, which is acknowledging the "flow" of the game. If a pitcher has completely throttled the opponent for several innings, to an extent you can throw away the binder and/or the pitch count. Whenever the manager arbitrarily brings in a reliever or a group of relievers, the odds are that at least one of them will not have "it" that day...which is exactly what we saw yesterday. But Boone compounded that initial faux pas by continuing to allow Lasagna to pitch to batters even after it was obvious to everyone except him, that Lasagna was missing over the fat part of the plate and the Sox were hitting rockets off of him..having good stuff means nothing if the pitcher has no control and is not hitting his spots. But to be fair, the defense also spit the bit yesterday...Judge would have likely made both plays in RF that Allen butchered...and IMO, Torres could have easily nailed the eventual go ahead run at 3B on an easy grounder, but threw to 1B instead.
