@Cyan I did some testing and figured something out !
cIOS configuration:
base 56 => 249
base 57 => 250
base 58 => 251
USB Loader GX 3.0 r1272 (normal version) with default settings
Loader IOS: 58
Game IOS: 249
=> Boot WiiU with only vWii HDD connected
=> Go into vWii mode, launch homebrew channel, then USB Loader GX
=> Works !
=> Go back to vWii Menu, plug in WiiU HDD, homebrew channel, start USB Loader GX again
=> "USB device not initialized, switching to channel list mode"
=> Go back to WiiU menu, then launch vWii menu again, homebrew channel, USB Loader GX
=> "USB device not initialized, switching to channel list mode"
=> Set Loader IOS from 58 to 249 in USB Loader GX settings
Now I try again but this time with Loader IOS 249:
=> Boot WiiU with only vWii HDD connected
=> Go into vWii mode, launch homebrew channel, then USB Loader GX
=> USB Loader GX freezes on startup, Kill WiiU power
=> Boot WiiU with no HDDs
=> Set Loader IOS back to 58
=> Go vWii Menu, Plug vWii HDD, Homebrew Channel, USB Loader GX
=> Works !
=> Set Loader IOS to 249 again, Homebrew Channel, USB Loader GX
=> Works !
=> Go vWii Menu, Unplug & Replug vWii HDD, Homebrew Channel, USB Loader GX
=> Still works !
=> Go vWii Menu, Plug WiiU HDD, Homebrew Channel, USB Loader GX
=> Actually works this time with both HDDs !!!
=> Go to WiiU Menu, launch vWii menu again, homebrew channel, USB Loader GX
=> USB Loader GX freezes on startup, Kill WiiU power
=> Boot WiiU with only vWii HDD connected freezes USB Loader GX on startup again
=> Set BootOS to 58 in meta.xml in SD card
Now this time with BootOS set to 58 in meta.xml:
=> Boot WiiU with only vWii HDD connected
=> Go into vWii mode, launch homebrew channel, then USB Loader GX
=> Now actually works
=> Go vWii Menu, Plug WiiU HDD, Homebrew Channel, USB Loader GX
=> Also Works !
=> Go to Wii U Menu, then back to vWii menu, Homebrew Channel, USB Loader GX
=> USB Loader GX freezes on startup at "reinitializing devices"

=> Boot WiiU with only vWii HDD connected
=> vWii mode, plug WiiU HDD, homebrew channel, USB Loader GX
=> USB Loader GX freezes on startup at "reinitializing devices"
=> Same when booting with both HDDs connected
I figured out that USB Loader GX (with Loader IOS249 & Boot OS58 both are necessary!) needs to be started once without WiiU HDD connected, only after that it can be started with the WiiU HDD connected. If it's started for the first time after boot with WiiU HDD directly connected on boot or WiiU HDD plugged in on vWii menu, it will freeze in both cases.