This is an interesting question. As far as flexibility, it is a moot point as others said above.
As far as sound quality difference, I can relate to this first hand although with different models. A friend of mine has an MA6400 integrated from a few years back. He just loves it and had me audition it. I immediately began looking of one but to no good avail (I had to have it NOW and did not find one). I then bought the separates that make up the MA6400/6450: the C712 and MC7100. There are many reviews online about how awesome the MA6450 is but no one really says anything about the separate version. I borrowed the MA6400 I had first listened to and compared, head to head, with the separates and I COULD NOT hear a difference or tell them apart. The separates version in this case has a little more power but the sound quality is equally sublime. So, if space and extra cost are an issue, go with the MA6900. It is a heck of a deal compared to MC202+C42 and judging from my experience, they will sound identical (actually they are identical circuits so this is pretty much a given). They are simply beautiful pieces that make the most beautiful music I have heard.
As far as sound quality difference, I can relate to this first hand although with different models. A friend of mine has an MA6400 integrated from a few years back. He just loves it and had me audition it. I immediately began looking of one but to no good avail (I had to have it NOW and did not find one). I then bought the separates that make up the MA6400/6450: the C712 and MC7100. There are many reviews online about how awesome the MA6450 is but no one really says anything about the separate version. I borrowed the MA6400 I had first listened to and compared, head to head, with the separates and I COULD NOT hear a difference or tell them apart. The separates version in this case has a little more power but the sound quality is equally sublime. So, if space and extra cost are an issue, go with the MA6900. It is a heck of a deal compared to MC202+C42 and judging from my experience, they will sound identical (actually they are identical circuits so this is pretty much a given). They are simply beautiful pieces that make the most beautiful music I have heard.