Certainly, retracing my steps:
Preferences -> Atari -> Atari Type -> Atari XL Ultimate 1MB
Preferences -> Expansions -> XL Ultimate 1MB/SIDE:
- Ultimate 1MB flash file: ultimate.rom (v3.10 from Flashjazzcat's web site)
- SIDE2 flash file: side2.rom (v3.0, also from Flashjazzcat's site)
Where I believe I may have stumbled during my first attempts was:
Media -> 'Handle Special Cartridge' -> Insert SIDE2 (CMD-I) - first it took a while to realise that I had to do this, then I found that I had another rom file for SIDE 2 that was apparently not fit for purpose.
Remains for me to understand:
I cannot use FDISK, or rather it does not find any APT devices. Still, I have the VHD that I created for Altirra and it works fine, both the FAT and the APT parts, so I currently don't have to use it. Been changing the SIDE2 switch between SDX and Loader, but I am not more enlightened than before.
Please let me know if there is anything else I can do to help. Screenshots below in the spoiler section.