"Better" Snook? I don't know about better. But from a theoretical and analytical design approach, a two box solution may have benefits over a one box. No matter how good your transport is, whether it be a transport or player, or, a top loader vs. front loader, it will generate mechanical vibrations. This condition is not always the fault of the transport itself.
Many times in the actual CD, the metallic wafer "sandwiched" between the plastic substrate, is not held to tight tolerances relative to each other. I am speaking in terms of concentricity. The metal portion in essence becomes an "eccentric". The results are an out of balance condition very similar to having a tire out of balance on your car.
This can be a very challenging condition to ANY type of transport mechanism. The major problem being transfer of transport vibration into the unit's chassis and ultimately, D/A-A/D circuit. Crystal oscillators (time clocks) in the DSP circuits, HATE externally induced vibrations. "JITTER". Audio designers focus heavily on addressing this problem. I personally feel the ultimate solution is two box. Needless to say, the transport can't vibrate what's not there. Bad enough you're already battling airborn and structure born vibrations in the listening environment.
Although, the two box can also be a double edged sword if the interconnect between the transport and D/A isn't up to snuff. Impedance level mismatches can, and will induce jitter. Fortunately, the Audiomeca gear provides true balanced connectors for digital throughput. In the case of 75 ohm connection (RCA), it is SO important to have a TRUE 75 ohm digital cable W/ TRUE 75 ohm connectors.
In regards to the Audiomeca "X" series updates, both the new Mephisto and the Enkianthus incorporate Anagram's/Analog Devices latest 24/192 Sharc upsampling based technology. You will absolutely hear a difference in sound quality, detail etc, between the newer "X" and the older gear.
One box vs. two box? Let your ears be your guide. But, I will almost bet you'll find the Audiomeca two box to be a little quieter, a little more detailed, with a much cleaner bottom end. Let us know what you find.