I don't think it's fair to say their method is a one-style fits all philosophy. They definitely have a preferred style for pitchers - strong fastball control, change up, and one strong off speed offering - and that's what they target in the draft, but I don't think they limit their prospects or take away things they do well if they happen to find someone who does other things. They aren't grabbing all the pegs and then jamming square ones into their round hole. They are instead focusing on adding round pegs.
Offensively, I don't think there is anything resembling the approach that we see with the pitching. I don't see any real consistent focus in the draft for a certain type of hitter.
Whatever they've been doing over the years developmentally certainly hasn't been successful. But it's hard to pinpoint at exactly which point in the process have things broken down and assign blame. Is it scouting? Is it development? Is it bad luck? Is it physical training and keeping guys healthy? Is it just on the players themselves for not developing?
You saw this with Joe Jordan. He loved to draft speedy 4th OF types, hoping they could develop into everyday players. Think Hoes, Avery, etc (I used to have a list of like 10 guys whose names escape me now).
With pitchers, what you described is basically what any team looks for in a starting pitcher. Changeup to get opposite handed hitters out, breaking ball to get same handed hitters out.
The O's don't seem to have a philosophy to me as much as a team like the Twins used to. They only really targeted plus control guys with 4+ pitches (Perkins, Blackburn, Baker, etc)
The Orioles like two types of pitchers it seems. Sinkerballers and power arms. Harvey, Gausman, Bundy all fall into the power arm group. Mike Wright, E-Rod, Zach Britton are groundball types.
There's a difference between having a system for evaluation and promotion and instruction. The Cardinals, Rays, Rangers, etc. all have systems for evaluation & promotion where they evaluate players based on criteria drawn up at the beginning of a season or call up. This gives the player and org. specific goals to achieve before moving players around. This creates better communication, and means all players/coaches are on the same page.
The Rays (and other teams, like the O's) have instructional systems where they decide what type of instruction a player will get, regardless of who they are. There are obviously exceptions, but there are general guidelines. For the O's its biomechanical analysis, tweaking their mechanics to fit within predetermined norms based on that, and no cutters it seems.