The EEPROM layout can't be different since the PC-based tools access it directly, and the counterfeit chips would simply not work for anyone who puts their own Manufacturer string in them etc. The "command sequence" is completely PID-agnostic on the wire. What goes on between the USB host and the FTDI device is a control request to write an EEPROM byte at a certain address. The chip doesn't care about the meaning of this byte until it's power cycled, and even then, it won't care if the CRC at the end of the configuration area is wrong.
So, I back out of my claim the FTDI merely does a wrap-around to erase the PID. It also has to update the CRC, since otherwise the chip would ignore the contents of the EEPROM and start up with default VID, PID and other configuration. What they do is very much deliberate.
As for the chips with the built-in EEPROM, as I've stated, it's rather simple to attach an external, pre-programmed EEPROM. Heck, perhaps it'd be a good thing to offer as a product for people who wish to unbrick their devices - as long as the counterfeit chips implement this. Perhaps the counterfeits don't implement it, though? I really wonder how much do the counterfeit FT232R chips do as far as emulation of the real FTDI chips. Do they, for example, offer the clock outputs, like the real FT232R chips do? I bet they don't, and I bet that it'd be rather trivial for an amateur to check if a given chip is real or not by doing one well-placed behavioral test like that (specifically, set one CBUS output to 48MHz clock). After all, the counterfeit chips are really just a standard microcontroller with masked ROM. How many mack-programmable microcontrollers can output the system clock on one of 5 GPIO pins? The counterfeits aren't custom silicon, after all.
While on that topic, I have to check if some FTDI chips that I have with wildly off-spec silicon oscillator frequency are genuine or not. If they aren't, DigiKey is gonna get some talking to :)