Pre-game warm-ups are accounted for in the recommended pitch counts by ASMI. Warming up is factored into the numbers that they came up with, so you never include them in the pitch count equation. In fact, warm-up pitches between innings are also taken into account in the recommendations. The ASMI recommendations only refer to in game pitches to batters.
How many pitches has ASMI assigned as "warm up" pitches? 10, 30, 50, 100???
Why hasen't ASMI (American Sports Medicine Institute) come out with recommended throw counts for catchers? Obviously they have strong opinions about pitch counts to protect an arm and things not to do, we see these rules mimicked in tourney rules...but if every catcher throw back is equal to 1/2 a pitch where are the rules to protect the catchers arms in those tournaments?
It isn't an exact science, nor a "hard" pitch count. Heck, even LL allows a kid to finish a batter after they reach their "limit." If the recommendation is 100 pitches, then 105 or 110 isn't that much of a difference. The idea is to prevent 120-150+.
As for catchers and other position players, there is a difference between pitching and throwing. Pitchers are throwing max velocity on every pitch. Catcher's do not. Trying to equate it to some percentage of a pitch is difficult at best. So while pitching too much can clearly cause problems, the question is, is there evidence that throwing too much is problematic? We have all heard the saying, kids don't throw enough.
IMO, the biggest thing with catching and pitching is fatigue which is really what leads to problems.