I'm really sorry, I admit my description was quite confusing. All of
this is not exactly a problem to me, I could just format the pendrive
with the desktop BIOS geometry 974/128/63 and be done with it. I am
just being stubborn, trying to understand if there is a technical
reason that FreeDOS refuses this convoluted setup, while the other
loaders accept it, even MS-DOS. The following is not in chronological
order.

I have created a tiny 8 MB partition in the end of the desktop's hard
disk. I can boot FreeDOS from there and I also have copied Grub4dos
files to this partition.

My pendrive has syslinux in the partition boot sector. I have copied
FreeDOS files to its root and tried to chainload into it. Only on the
notebook everything works fine, because it sees the same geometry as
in the MBR. On the desktop syslinux boots, I can chainload FreeDOS
kernel, there is the expected WARNING about geometry, but COMMAND.COM
cannot be found on the pendrive partition. I must point it to the copy
of COMMAND.COM on the hard drive partition.

When I load FreeDOS from the hard drive, the pendrive partition gets a
drive letter but I cannot list its contents correctly. From here I can
run Grub4dos on the hard disk, then in its command line I can list the
contents of the pendrive. I can also:
- chainload the pendrive boot sector to get syslinux boot prompt. Then
I use the chain.c32 module to
    - load FreeDOS from the pendrive
    - or chainload back into the hard drive partition.
  Except for swapped partition letters and drive numbers, it is the
same as booting from the pendrive.
- memory-map a floppy image with FreeDOS. Same thing, pendrive inaccessible.
- memory-map a MS-DOS 7.1 floppy image. It can see the pendrive correctly.

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