Is there any reason why domain\username can’t be passed over to freeradius as it would make connecting to wireless much simplier as Windows machines usally try to SSO using that.

It would also then allow machine accounts to login.

I can only guess that it was not implemented for the use case you have in mind.
Assuming that you already have seen the Wiki entry with its notes on debugging I’d recommend to add an enhancement request on forge.univention.org.

Took me a while to get around to it but bug 42535