Because this game relies so much on coaching points, the ratings aren't going to be 100% accurate all of the time. The out-of-position people you put in for the O-line may have an outstanding O-line coach, with all sorts of special skills in pass-blocking, so that may skew the results.
Also, I read that in Madden the ratings actually don't go below a certain threshold (i believe it was 40) no matter what. So if you put a safety at the guard posistion, his pass/run blocking rating will actually be 40 instead of, say, 12 or something. Can't remember why they did this, though.
Over a full season you should see a statistical difference but in one game you may not. I believe the developers wanted to make sure that a 70 something DE had 4-6 sacks a year, while the 90-something DE had 9-15 sacks a year (or something along those lines). Which if you think about it, over a course of a season, is not that big of a difference considering the amount of pass plays defensed (4 sacks over 450 pass attempts vs. 10 sacks over 450 pass attempts).
Also, as posted somewhere on this board, the developers stated that the realism of ratings increased if you play the game as opposed to supersimming, simming it. Playing the game used thousands of dice rolls, supersimming used hundreds of dice rolls, and simming used tens of dice rolls.
I ran the same experiement as you a few months ago, and got comically bad performances, so I'm OK with it, even if it's not perfect.