From the installer page:
2. Poor cartridge connection - data will be interrupted if it crashes
Aside from seating the 64Drive and loading a normal game ROM is there any other way to ensure a solid connection? If I am able to load Mario 64 and run around the castle for a minute should that be validation enough that I can begin the firmware upgrade?
I read that as there being a poor cartridge connection issue during the data transfer. As in, you bump the cartridge during the transfer. If you're able to get into the 64Drive menu and load the upgrade ROM and start it, you'll be fine, just make sure the N64 is on a stable surface and that there is nothing that can fall on the cart.
I'd really only be concerned if you've had corruption issues before that you know aren't related to the ROM. If you're not sure if you've seen a corruption issue, you probably haven't, as they're typically very apparent (severely deformed models, shrieking high-volume sounds, etc.)