You know, I've always wondered the same thing. I don't know that adjusting levels via the recording device's line-in would affect the sound as it's not applying any gain like the internal mic pre-amp would. Maybe some engineering geek can clue us in better
Note though that switching levels on the MMA causes a click in the recording as the knobs are moved. I always set my gain on my MMA ahead of time then make fine adjustments with my MD's line-in adjustment. Also, it's sometimes hard to tell if both knobs are set equal on the MMA. I've always pondered this same question though. I bet even if there is a difference in quality, it's minimal.