I can try to answer this question from the perspective of my Sony project, where I took cues from pro modders like Reference Audio Mods, VSEI, and Richard Kern, and added my own tweaks. In selecting a mule platform, the analog section of a CDP doesn't matter much, as it is typically replaced. I believe pro modders select their mule platforms based on the quality of the transport section circuitry (not so much the the opto/mechanical elements, which as you point out are typically unmodified Philips; custom opto/mechanicals such found in the SCD-1 or the new Esoterics may be better yet.) There is fairly wide divergence between original manufacturers in the design/execution of transport circuitry. This becomes a gating factor, as these circuits are difficult to modify given the complexity of the VSLI chips & the high density of surface-mount components. So in order to obviate the problem of redesign, modders select transport sections with well-designed circuits and concentrate on mods to power & perhaps replacement of the master clock & parts-bin quality surface-mount components in the critical paths. I bet Zanden and the other hi-end transport manufacturers take a similar approach based on OEM circuit boards.
Modifications to power make a huge difference in the performance of the DSPs. I learned that even the best AC/DC discrete DC regulation I could find in the aftermarket could not match the sound of batteries, together with increased capacitance at the application and discrete DC regulation in place of stock cascaded 3-pin regulators. The best sounding batteries have low internal resistance in the 2 milliohm range-- which cannot be obtained with compact batteries such as alkaline, NiMH, or lithium. To get to this level you need high amp-hour, sealed lead-acid batteries with thin-plate technology, such as Odyssey PC2150 or Optima Yellow Top. Their size and weight would limit their appeal to commercial manufacturers. Also, it's critical to attend to DC trunk wiring of adequate thickness & quality and to use fast filtering capacitors at the application. I can't imagine that hi-end manufacturers with more portable battery-powered components can achieve this level of performance. I LOL at photos of the bank of D-sized alkalines inside a Sutherland phono stage.
Finally, the ability of the tranport/DAC combo to work together at a high level will be limited by the interface (I2S, PDIF, clock-link, etc.) One reason why I decided to mod a CDP rather than a combo.
Dave
