Bringing in AJ Cole was PART of the baseball strategy. When you take out pitchers who are already performing well, you are relying on other pitchers who you have no clue will perform on that day.
The Jays have managed their teams like they've had elite bullpens like the Rays when we know the actual reality. Treating players like they're robots is part of the problem. If you've ever played a sport on any level, you know there are days you feel great and days you feel crappy, Jays have not incorporated this into their logic.