I can confirm what you were told.
My hubby and I are serving separated (again!). I have the MQ and he lives in the mess at the other end of the country. I pay for the MQ and he only pays a reduced (£2.75 per day I think) rate for food but definetly no accommodation charges.
We have swapped around and when I lived in due to forced seperation it was the same. He paid for the MQ and I only paid reduced food charges.
Unfortunately I don't know where the reference is but I'm sure your adminners should be able to help (!)