Without knowing the Apogee product you're using, the quick answer is yes. If you did nothing to the tracks but a D/A and an A/D conversion, you could hear the results of the conversion, and the effect of the recording device(s). If input was about the same as output then you'd have your answer. The rack and the Masterlink would be what makes the difference. My music partner uses Apogee in and out and he's very happy with his results.
Love, it's something that we do.
I'm David McMillan. My friends call me Chuck.