Yeah I think it was just the developer working with what he was familiar with. For example, the emulator used for the 3DS NES Virtual Console titles was develop

Yeah I think it was just the developer working with what he was familiar with. For example, the emulator used for the 3DS NES Virtual Console titles was developed by a different team at iQue. It uses its own bespoke header format called TNES rather than the standard iNES header.