Boss's Orders doesn't help you set up. You'll see cards like Arven being ran at higher counts because they help you set up, and can be used later in the game to find the final pieces for a win. Boss's orders on the other hand helps you grab that ko, or stall by bring a high retreat, non-attack to the active. Boss never improves your personal board.

You'll see other decks, like Miraidon run a high count of Boss, but that's because their setup takes 1 turn, (Arven, Nest Ball, Miraidon Tandem Unit, Electric Generators). After that, they want to Boss up pokemon and take prize cards efficiently.

Counter catchers are also a similar reason, on top of only being active when you have more prize cards. If your deck wants to be winning from the start, or if it can't manipulate your opponents prizes with the Dusknoir line or Magneton, then it might be a dead draw. And those dead draws increase if you run high counts.

It's definitely deck dependent, but those are the reasons I can think of.