That can't be right - the .bin file that comes out of the 2.1rc2 zipfile is ~100KB in size (almost precisely the same as the Updater utility in the 1.65 driver package), there's no way the EPROM is that big. At a guess It's probably no more than a few kb. Unless of course it's reprogramming the main Xilinx FPGA's onboard the card.... but I would doubt it.

There don't appear to be any options to speak of with the 1.65 Updater utility when you run it - nothing from the menu that appears to give the ability to change while rom file it is uploads. The only thing it appears to allow you to do is hold space after clicking it in order to force a Nubus slot number.