The PCE doesn't use a 6502 though. Honestly if you have enough money, and it would be a lot, there is nothing stopping you from paying a company/lab to do the work to break it down and make it possible to clone it exactly. I want to see a DUO with SGX support and native S-Video & RGB output as well as Region Switching. That would be nice. But I don't know that we will ever see that. Something more likely is like those FireCore Genesis clones. Essentially it's a device that is just built to run an emulator but it can use real media (cartridges). You could probably build a system like that for the PCE.
Those don't emulate, at least not in the traditional sense. They're clone hardware. They use a GOAC, Genesis On A Chip, which is engineered to perform the functions of the Genesis at a level that is "good enough". They do probably have a pretty legit MC 68k knock-off core. It's the other functions that are usually a bit off due to them replicating things cheaply and in poor detail.
As for the PCE, the PCE CPU is a modified 65C02. There are schematics and markup files for the 6502 and, I believe, the 65C02. If you use those as a base you have a good portion of the core of the PCE's CPU already.
Here's some of the goodness I've already found...
http://www.visual6502.org/