As I've mentioned numerous times before, this system is going to be somewhat flawed. The sim only allows for very few characteristics for which to grade these players. The defensive line, for example, allows grades for Run Defense and Rush Defense only. And within those categories they can only be ranked 1-9. Therefore a player ranked high (such as Freeney at #20 overall) will have more points to distribute than a guy like Trevor Pryce #39 overall. So even if I max out Freeney as a Pass Rusher, he is still going to have some points available and the only place to put them is in the Run Stuffing category. It doesnt accurately reflect his game, I get it. But there was no other option. So yes, you are correct that its not accurate. But that's the way this game is set up.
As for Bobby Mitchell, yes the sim bases his RAC on YPC. I also agree that's not really a reflection of RAC. But again, that's just the way this is. It should probably be renamed something different. Mitchell's YPC was 15.27, which was nothing special. Ranks him 76th out of the 144 players ranked. So, that's the ranking there.