For Dragon Age 2 and Mass Effect 3, I agree with their reasoning. Steam doesn't allow in-app purchases that circumvent their distribution system, and that's a load of crap.
The idea there is probably something along the lines of preventing developers from selling their game for $0.99 and "unlocking" it in-app for $59.00.
The no in-app purchases which don't cut in Steam was introduced when they began allowing free-to-play games on the service (which are usually monetised by microtransactions, and would be a money-loser for Valve if they didn't make a cut from them). I don't know why Steam can't make an exception for EA titles (or those purchased from the store rather than F2P), but that's the reasoning.