Okay ... after a week this has been viewed over 1400 times with no reply. I guess that no one else is sure.
Maybe the following will help someone else:
I've scanned through the BIOS release notes, and in version 0035 I see the following:
o Fixed issue where no video is displayed if both PCI and PCI-e VGA cards are attached and primary video output is set to integrated graphics.
- I deduce that this means that any card can be installed in the PCI or PCI-e x16 slot, and the internal video should still work.
o Fixed an issue where some PCI-e x1 cards would not work when plugged into the PCI-e x16 slot.
- From this I deduce that any card can be installed in the x16 slot (I don't know of any x1 graphics cards!).
So, I assume that I can install a SATA/RAID HBA into the PCIe x16 socket, that it should work okay and that it should not disrupt the function of the integrated graphics controller. I guess that my next step is to purchase such a card and try it!
I purchased a SAS/SATA HBA - well, a Supermicro AOC-USAS2-L8i RAID card using their proprietary 'UIO' layout (actually, just a PCIe x8 card built back-to-front), and it is working perfectly well in the x16 slot with no obvious untoward interactions with anything else.
So, this answers my original questions.