You are basically correct in my book. Some CD Players made excellent transports, but I would not buy a new Alpha and then the MSB. There is a $80 Aiwa CD Changer that makes a decent transport, so save your money.
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Npotter- I would suggest that you not discount the importance of a good transport in the overall sound of a transport/DAC combination. Also, the platform under the transport will have an effect on the sound(vibration equals data errors/corrections). The DAC's performance will be limited by the quality(accuracy) of the data that is fed to it. Yes, a simple transport will produce sound, but rarely the emotional connection found in music. It all comes down to your expectation level based on the quality of the rest of your equipment. Just MHO. Goodluck.
I've owned both CD Players and Transport/DAC combos. My current front-end is a Roksan Caspian CD Player. A pretty good player (it ought to be at $1600). My previous rig was an MSB/(very old) McCormack transport. I thought the Roksan was better; and that is why I "upgraded". Currently I am auditioning an MSB with upsampling/Aiwa changer combo; the Aiwa was recommended by the Chicago Audio Society (I think). Separate DAC and transport are more "easily" upgraded (at least in theory). Admittedly though, I'm not sure the MSB/Aiwa is an improvement over my Roksan; though it is considerably cheaper. Where I am going with this is, I'm not sure there is a hard and fast rule that Transports/DACs are always better than one-box players or visa versa. Audition both the Alpha and the MSB. Buy what satisfies your requirements and budget. If you decide on the player you can always "upgrade" to an external DAC later.
Gallaine- I agree with you on the idea that separates aren't always better than a properly implement CD player. Though more expensive than the units previously mentioned, the Cary 303 and the Electrocompaniet EMC-1 are just two examples of outstanding CD players at their respective price points. On the used market, both are bargains. Just MHO.
If you're just starting out or looking to upgrade from a low cost cd player, then I think the transport and dac route is the way to go. It gives you more opportunities in the future to upgrade as technology evolves and/or prices go down. Also, there are some great deals and values available today in dacs and transports. However, I think you need to factor in a low cost jitter reduction device to get the best performance. For digital cables, you can start out with Apogees and upgrade later. I have been using the Aiwa changer for about a month and a half. Right out of the box, I was a little skeptical about it. (It certainly looks "different" when its playing with its flashing lights). For about 5 days, it would not lock into the secondary lock on my Audio Alchemy DTI pro but then it
seemed to stabilize. After about a month a half of use, the sound seems to have fleshed out some. Right out of the box it seemed a little lean and I had to compensate by changing some cables. Now it seems a little richer and I am going back to a more revealing cables into my dac and preamp. It still does not beat my Parasound CBT 2000 by any measure, but it's worth every penny of $80 or $90.