The question is if the system on the server or hardware failure after restoring a bare metal backup to a new machine what will hapen with custom programs and settings non microsoft in that backup, will it they work after restoring?
That's the million dollar question, isn't it?
...which is why backups should be considered completely useless until you've tested restoration successfully.
There's no obvious reason that non-MS software and data would be skipped, but this all is dependent on how you have things configured. Which goes back to the need to test restores.