From what I've read, the Apple 30-pin to lightning adapter actually has it's own DAC in it, and it's supposed to be pretty high quality. I was originally using an iPod Classic plugged into the AMI 30-pin cable and it didn't sound that great. I switched to using a current generation iPod Touch with the 30-pin to lightning adapter and it was noticeably better. This is on the stock MMI system + an upgraded processor, amp and speakers that are very revealing of audio quality.
I don't think you're going to notice much difference with an external DAC + line in, and you'll lose the ability to browse playlists, skip tracks, etc on the MMI...and then crash into the back of someone messing with your iPod or iPhone.