I have spent far more time on this question than it deserved, and wanted to document what I had learned, so answering here.
1) Flashing the BIOS.
The easiest way to flash a stock bios is from within the BIOS using Q-Flash. I found that selecting Q-Flash from within the full BIOS was more successful than attempting to launch Q-Flash from the boot screen. If you are running TPM/Bitlocker, please make sure to suspend Bitlocker protection (see below) before upgrading the BIOS.
However, with TPM/Bitlocker enabled, flashing under Windows will not work. To work around this, type "Bitlocker" at the start menu, and then select "Manage Bitlocker". You can then "suspend protection" on the boot drive. Reboot the machine, and press DEL at the appropriate time to enter the BIOS setup. Disable the onboard TPM module, save BIOS settings and reboot. The computer will then boot into Windows. Running the Bitlocker control panel again will reveal that Bitlocker protection is still disabled.
The @BIOS flash program should now allow you to install a stock ROM. This appears to reset all your BIOS settings, but you can save them to a USB stick from within the BIOS before you start, and restore them afterwards. Don't forget to turn TPM back on if necessary. Bitlocker will not protect your drive until this is done.
2) Flashing a boot logo.
The bad news is that @BIOS boot logo features are even more flaky than a standard flash. The utility comes with a copy of AMD's changelogo command line utility, but unfortunately, Gigabyte appear to store checksums in an unused area of the BIOS, and a BIOS with a changed logo created using the utility will not flash, presumably because it has not had the right checksum information written into it. This is a shame because it means Q-Flash cannot be used to flash a BIOS with a modified image, and there is no way to get @BIOS to write a verified modified image to disk that I have been able to find.
However, using changelogo64.exe from the @bios install directory, I was able to determine the required format of the logo file. Since @bios doesn't report why the logo flashing process has failed, this should help to determine whether or not you have an image file in the correct format. I have had success with the following image settings
JPEG (compression level not important, but I recommend 90% compression to keep file size down).
Do not use interlacing when saving the JPG file, as this is not supported.
Bear in mind that the Windows loading animation will appear over the image, centred roughly at 400x515 (from the top left, so you may wish to keep an area around this point black).
If you are using TPM/Bitlocker, you will need to perform the steps described above before flashing, otherwise no amount of tweaking will work.
When you have a file in that format, things will still inexplicably fail. I have had more success using an BIOS image downloaded from Gigabyte and the "update from file" tab of @bios, but it may take a couple of attempts to successfully load your logo image. I have loaded the bios file, then the logo image, the logo image load process has come back with an error, and then I have reloaded the same file with success. Gigabyte tell me that they cannot reproduce the problem on their end, so do not seem to be able to fix this. It does not always work, and it may be necessary to try a few times over a few days until you get the BIOS image and the boot screen image to successfully load.
Once both BIOS file and boot logo image file have loaded wihtout error, and if TPM/Bitlocker is disabled, you should now be able to continue through the process of flashing using the @bios software.