I have not heard the Music Two, but have heard the SD2, and have heard several acrylic demos that use the same driver units as the Music Two. Even aside from the fact that I haven't physically heard the Music Two, this is going to be a tough comparison because the SD2 is highly tip-dependent. It can sound quite veiled with the wrong tips, but with the right tips, will sound quite transparent. The Music Two is of course, custom-fit, and so only has one single signature.
If we compare the SD2 at the very peak of its performance potential, then I'd say the two are about neck and neck. The Music Two will still have more accurate sounding mids, the SD2 will warmer in the upper midrange, but the SD2 will probably appear to be a little teeny bit finer-grained sounding because it has very clean distortion throughout the vocal band, thanks to its Knowles GQ drivers. It will also have a miniscule amount better bandwidth on either end. Both attributes, distortion and extension, are probably extremely difficult to tell, or even inaudible. For example, even though the drivers for the Music Two have more intrinsic distortion than the drivers for the SD2, both are well under the hearing threshold for distortion. That's why I say that the two are neck and neck. On a macro level, the Music Two will sound, tonally, more accurate, and impart better vocal clarity because of its overall frequency response, which has a better balance of upper mids to lower mids than does the SD2. The SD2, on the other hand, is better suited for monitoring, where a less delineated sound helps smooth things over for long listening sessions. Again, small differences that are hard to qualify.
For me, what it boils down to is fit --- universal-fit IEMs, unless it's with a super-deep, secure fit like the ER4, have trouble getting to "optimal performance". The SD2 is a perfect example of that. I get really great fit rates with the SD2 --- it's about as comfortable and isolating a universal IEM as I've ever used, but it's so incredibly tip-dependent. Changing different tips drastically changes the sound signature and changes the treble resonances that occur within your ear canal. With a custom-fit option, you don't get those issues.
The SD2 is a very nice product; probably the best in the StageDiver line, but I find that when push comes to shove, I would opt for the better fitting IEM, which is a CIEM like the Music Two. Despite its great comfort and overall excellent design, it's hard to get the SD2 up to its best possible performance without fidgeting around a lot, and switching a lot of ear tips.