Look, I'm not gonna comment on the "ref issue", I have an opinion, but it doesn't matter for squat now. However, if you're gonna try and make a realistic argument about this, you need to allow for minutes played (and/or shot attempts in your statistics). For example, Duncan average 34.5 minutes in the regular season, and 41.5 against Dallas. He averaged 20.6 FGA in the dallas series, vs. 14.8 regular season... This kind of thing may account for a LOT of the variability you are seeing. It's realistic that his FTA/Game went up with his shot attempts.
Similary, Dirk averaged 19.3 FGA per game in the RS, 15.7 FGA per game against SA, and took 17.5 FGA/game against Miami. His shots went down, and his FTA/Game went up? Weird...
Wade, 18.8 FGA/Game RS, 23.16 fga/game against Dallas.