For the record, I managed to create a working HDD image from within MiSTer with the following instructions. You need a bootable MS-DOS floppy disk:
1.
Open up a shell with F9
2.
Navigate to the desired path
3.
Run the following command:
$ dd if=/dev/zero of=image.vhd bs=516096 count=N
This will create a file named image.vhd which is about 2 * N MiB in size. The number 516096 was chosen to match the size of a cylinder that has 16 heads and 63 sectors (16 * 63 * 512 bytes per sector), because to my understading XTIDE likes to address disk images by using the maximum allowed amount of heads and sectors per cylinder but you can use whatever number you like, the final image will be count * bs bytes large.
4.
Open the PCXT core
5.
Mount the bootable MS-DOS disk in Floppy A: and image.vhd in IDE 0-0. For some reason, this won't work if the HDD is mounted as a slave.
6.
Boot from A: and run:
A> fdisk
Create a primary MS-DOS partition, use all the available size. fdisk will reboot.
7.
If you need the disk to be bootable, boot again from A: and run:
A> sys c:
(if it doesn't work, you may have to format c: /s)