Using command-line to boot into primary and secondary ROM of MultiROM
I searched for the string multirom --boot-rom and came across an interesting paste (copy) posted by an untitled guest, with these relevant lines:

&lt;alvinmobile&gt; How do you autoboot other rom in a secondary rom?
&lt;alvinmobile&gt; I mean where do you store the info?
&lt;Tassadar&gt; it runs &quot;multirom --boot-rom=nameoftherom&quot; in su shell, and MultiROM takes care of that - it loads ROM list as usual and either directly kexecs the required kernel or sets force-autoboot into rom X (which saves into multirom.ini) and reboots

I was on the right track as it seems. I suddenly realized that multirom installer zip may be the final piece of the puzzle. And it was, since it contains the multirom binary and uses extract_multirom.sh script to place the binary et al into /data/media/0/multirom (accessible with root access only).
As for finding the name of a ROM, it is what you see in the ROM list in the app or the name of the top-level directories under /data/media/0/multirom/roms.
Boot into the ROM
(Prefix adb shell in commands if you want to use adb to test them.)
The command is very simple:
su -c /data/media/0/multirom/multirom --boot-rom=ROM_NAME

Replace ROM_NAME with the name of the ROM to which you want the device to boot into. It is case-sensitive so Internal works but internal doesn't to boot into primary ROM.
I've not tested passing a ROM's name consisting of special characters but whitespace can be escaped using '' and \. E.g., the name Xenon HD can be passed as 'Xenon\ HD' and  the whole command would be
su -c /data/media/0/multirom/multirom --boot-rom='Xenon\ HD'

You can create a symlink for convenience.
Trial and Error
With a bit of testing, I reached the conclusion that the ROM can be switched by editing the multirom.ini file alone, followed by an ordinary reboot instruction. Among other lines in that file, these are the most useful ones:

current_rom=COS12
auto_boot_seconds=5
auto_boot_rom=Internal
auto_boot_type=0

Here,

current_rom - contains the name of the currently active ROM or the last active ROM if the device powers off without an instruction to be switched into an another ROM
auto_boot_seconds - timeout to boot into default ROM
auto_boot_rom - the ROM that should be booted into after timeout
auto_boot_type - governs whether there should be a direct switch between ROMs or should the UI for ROM selection be shown during boot

(There are no sources to support the claims. I've reached the conclusion based on my experiment only.)
Let's assume that your active ROM is named COS12, internal ROM is named Internal and you want to switch to Xenon HD. Switch it this way:
(Requires Busybox)

su -c cp /data/media/0/multirom/multirom.ini /data/media/0/multirom/multirom.ini.orig       # one time command and optional, but it is safe to make backup always
su -c sed -i 's/current_rom.*/current_rom\=ROM_NAME/g' /data/media/0/multirom/multirom.ini  # for Xenon HD, ROM_NAME would be Xenon\ HD
su -c sed -i 's/auto_boot_type.*/auto_boot_type\=2/g' /data/media/0/multirom/multirom.ini   # changing to `2` causes MultiROM to directly boot into the ROM mentioned in `current_rom`. The setting would later be reverted to 0 after successful boot
su -c reboot

Commands are optional here. You can use a file editor app, such as QuickEdit to edit the file.
Note: During reboot:

If auto_boot_type is found 1, the ROM selection UI would be shown after boot logo and it overrides auto_boot_rom which means after timeout the device would boot into whatsoever the current_rom has, automatically.

If auto_boot_type is found 3, device would boot straight into whatsoever the current_rom has, but, auto_boot_rom would also now be found same as the current_rom. auto_boot_type later reverts to 1 after successful boot.
I cannot comment on whether this is a bug or a desired behavior, but this is how it is.


Further note that I wouldn't be surprised if methods mentioned in this answer fails for a non-Android ROM.