Is it possible to boot MOS from a FAT32 partition in X5000? How should it be installed/created? The latest installer disk and Hard disk tools does not seem to be able to do that....

As also Linux can be booted from a FAT partition (located on Sata, USB or BootSD disk) in X5000, there should not be a technical barrier.

The boot loader tries to find the required boot.img on the MorphOS default system partition. This loader only supports FFS and SFS formatted partitions. It is not recommended to use FAT32 for it as it misses support for various protection bits and has other limitations. So no, using FAT32 is not possible for multiple reasons.

@cyfm

The idea of using a FAT partition would naturally not be to load the whole OS but only the boot.img! That way you could use a disk controller card for loading the rest of the OS. As you probably know, in X5000 there are only two bootable Sata ports on the Cyrus boards, which causes problems if you want to use all the three OSs (AmigaOS, MOS and Linux).

Using USB disks in X5000 for booting MOS has also problems as you cannot use them without running first 'usb reset' command from UBoot cli (BTW, this fact should *definitely* be told in the installation instructions for MOS, now they are misleading).

Loading the boot.img first from a FAT partition on the BootSD would be the best solution to these problems.

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Of course I understand what you intend but that is not how the initial MorphOS bootloader works. It looks for a bootable partition to find the boot.img and obviously needs a complete system partition in the aftermath of booting MorphOS.
Currently, there are no plans to change that just for the sake of using FAT32 (or any other filesystem) to load the boot.img only at least. We supported similar ways of storing the boot.img on older systems like Efika and/or Pegasos but it was always causing trouble to update the system with the actual boot.img because it is difficult to identify the actual partition which stores it. With the bootable system partition as target, you at least have some semi-defined location where it is stored.
If you are experienced enough, you can always store the actual boot.img on the onboard SDcard directly and add a customized boot script to UBoot which loads it directly, just in case you want to go down this path. You are basically on your own once you need to update the boot.img firmware, though.

@cyfm
Thank you for the information! I have used MOS only a short time, so I do not know it very well yet, even less the history...

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Yes, that would be a little bit complicated... But do you know whether it is possble to define with UBoot variables what the "Start MorphOS" button in X5000's boot menu does? I have not found such variable with random trials... Or is the only way to edit the Uboot code directly...? What type checksum is used in it?

In UBoot code there is a string like this, which I suppose defines the default function for that button:

... Start MorphOS = setenv stdout serial,vga;.b..bootmorphos. ...

If the 'bootmorphos' command would be replaced with e.g. 'run mosboot', where 'mosboot' were a variable which could be defined using setenv as 'usbreset;bootmorphos', that would solve the USB boot problem.