What do you mean by instruction set? As far as I remember, Analogue physically looks at the chips under microscopes and recreates that physical design via FPGA (This is because the patents have expired, which is different from copywrite). You could be talking about bios (which I know of the Pocket, for example, they used their own, which included skipping the “Gameboy” animation when you first power on.), Analogue can just write their own BIOS that gets around it. (BIOS would be software, and thus classified under copywrite, instead of patent.)
Just to clarify, Jobst is talking about the sealed, high end gaming market. The used copy of Mario Party 3 you are waiting to buy is still $60. The open prices are the ones I care about, because they affect me the most (and I would wager, 99.9% of collectors).