Pins you are referring to (JTAG) most likely used during production for easy programming. There's no possible way 3DS can JTAG program any device, you need special programmer for that. Gateway doesn't have traced JTAG pins at all. Updating may be done by FPGA itself: it loads bootloader first, bootloader first looks for updates on sd card and if finds reprogram flash memory, and if there's no updates it loads firmware normally. DSTWO works this way, it only needs power from cartridge slot and all updating done by fpga itself (same proasic3, btw), you just need to insert card and wait few mins.