> [...]
> When running a system reconfigure and mounting this partition with
> ntfs-3g, which is FUSE, without rebooting, I can read and write data,
> but on reboot the system will fail to boot.
> 
> My initial guess is that this may be some
> issue with the FUSE kernel module not loading at boot time, but I have
> no clue how to add such entry to load it, if this is the problem at all.

Based on that guess I would try looking into the initrd-modules field of
the operating-system declaration. No idea wheter it will work but seems
like it would be worth trying.