Ray doesn't change anything (anything major at least. Any coach is going to tweak and suggest slightly more efficient movements and point out flaws) when they get to the majors, the pitchers are just unprepared to not get by on their natural stuff. AAA to MLB is like the jump from RK and A- to Hi A ball.
Those are the levels where coaching is very important. when you make the jump to Hi A, you leave behind the league where you can get by with a dominant FB and a single mediocre breaking pitch. The hitters that make it to that level can hit that weak breaking stuff and have a more selective eye. Similarly, the jump from AAA to the majors is another big step where a lot of organizational filler sits. At AAA a pitcher with refined natural stuff and passable control can a do a lot of damage without locating well and basic pitch sequencing. This is where I feel that the Pirates are dropping the ball a lot, mainly the pitch sequencing. They're having pitchers with very good natural stuff throw the organizational philosophy of "Get an out in 3 pitches or less" and it's not forcing the pitchers, mainly the starters, to sequence effectively since they can get some quick whiffs from bad hitters and/or a lot of bad contact on chasing pitches. So when they make that jump, they're not prepared to cerebrally attack hitters. A majority of MLB hitters are going to spit on breaking balls if you don't set them up properly and/or can't throw it constantly for a strike and sit on the fastball.
However, I think this approach is why they are able to churn out and maximize their bullpen arms. 3 pitches or less is basically a reliever's mentality and working with them to hone that allows any pitcher only going an inning or two to play up their stuff and have a reliever's mentality from the get go. They don't have to worry about seeing that batter again or having a repeat sequence being exploited later down the lineup.
This isn't to say I think Searage should stay. I've been beating the move on for Searage drum for about 3 seasons now. I don't think his method of fixing pitchers is working anymore, and hasn't worked since Benedict left for Miami. I believe Benedict was the one who was able to spot the talent that was ripe for Ray's treatment. With Ray and Jim, they hit big and often in reclamation projects with AJ, Liriano, Volquez, Happ, Vance Worley, and the first step of Charlie Morton as well as bullpen mainstays like Grilli, Watson, Justin Wilson, Melancon, Hughes, Blanton. Without Benedict most, if not all, of the Pirates' similar pitchers have flamed out (Lyles, Niese, Voglesong, Hudson, LeBlanc, Bastardo part II, Benoit, Rookie Davis).