After hours of skimming the help files, I managed to get my stick to boot DOS (Win9x) as well from the boot menu. I now have small and meaningless questions:
1) Does the tool make everything automatic but you still have to do it manually for a DOS option ? Or should I have put the files on the right place so that it would recognize I want the option activated ? (read "Or did I miss something")
2) The help file says Command.com should be in a \DOS directory but if only IO.sys and MSDOS.sys are in the root, it asks for location of the Command.com. (obviously solved by moving it to the root)--> is it something I forgot to do or an error in the help file (MULTI_CONTENT_Files.txt) ?
Thanks.

USB_MultiBoot5.cmd can make an USB-stick for direct Booting with MS-DOS from the boot.ini menu.
You only have to add IO.SYS and MSDOS.SYS to the MULTI_CONTENT Folder and
COMMAND.COM to the folder DOS of the MULTI_CONTENT Folder.

For Direct Booting with MS-DOS it is necessary to choose FAT Format with PeToUSB (max 2GB stick) and
to select Multi_boot.ini as boot.ini (option B ) and MULTI_CONTENT as Source (option 2) in the Main Menu.
The point is that the supplied config.sys of the MULTI_CONTENT folder regulates
that for MS-DOS the COMMAND.COM is found in the DOS folder.

For booting with FREEDOS all necessary files are already in the MULTI_CONTENT folder.

So the USB_MultiBoot5.cmd Program takes care of everything,
if you make the right selections and for MS-DOS has added the 3 mentioned files to the MULTI_CONTENT folder.

Thanks for your reply, sorry, I had quite a hectic and buzy week. RESPECT, man.