We've done this both ways (when we did not have consoles available, we had to modify the stock consoles).
Modifying the stock console is not a DIY job unless you have a decent amount of plastic fabrication experience. Because the factory console has the unique shape around the stereo, it cannot simply be "cut out" to accommodate the double DIN shape. In addition, because the surface finish is a metallic foil that is applied by heat transfer, this foil must be ground and sanded off first to prevent the edges between this foil and the new bonded in piece of plastic from separating after painting.
Once the metallic foil is removed, you then need to grind out the entire stereo section to the edge of the console. Next, bond in a compatible flat plastic stock. You must use a bonding agent to fuse the plastic together. Once bonded, you would then cut out the plastic stock for the stereo unit. Finally prep (making sure all of the foil has been removed) and paint.
This is a much more labor intensive process than simply cutting our composite console. I would expect to pay an installer at least 5-6 hours to do this work + the cost of prep & painting. The usual labor rate for a good fabricator is around $25-50/hr. Doing the math, and considering you get to keep the factory console at the end of the day (which is becoming an important issue to the resale of these cars as they become rarer) - I think the composite console is a good choice. For more info, check out this:
http://www.scienceofspeed.com/produ.../NSX/ScienceofSpeed/composite_center_console/
I would consider using the factory console however if you were instead planning on using a single DIN, and you wanted to keep the factory ash tray. Most buyers in my experience will want the factory stereo and console however, so there is still the factor of permanently modifying the factory console.
Cheers,
-- Chris