Yes, they still will. Like I said, you still have to follow directions. Specifically the step where it says to confirm that the firmware version in the emuNAND's system settings shows "GW3D X.X.X-XX" (where X = whatever the firmware version is). This is your confirmation that if you update without exiting the settings, you'll be updating the emuNAND not the sysNAND/realNAND.
Edit: But also keep in mind that exiting the emuNAND's system settings will revert you back to the sysNAND so when you go back into the settings, it won't show the firmware version starting with "GW3D" anymore, so that should alert the end user and they at that point should go back into Gateway mode to do the update.
Oh ok, thanks for clearing that up.
As some others, I want to be extra sure to know and avoid any issues, before tempering with the system.
But I also get your comment now, you would have to be especially careless and not read the directions that come with the firmware update, to do it wrong.