I was of the understanding that room upgrades for flight crew were at the discretion of the hotel and of no charge to BA but I could be wrong. I used to work at a crew hotel before I joined and we only got the same wholesale rate for each room, regardless of room type.
As for rest seats for flight crew, I can understand why they are needed but I often wondered about the loss of two revenue club world seats on the likes of SIN.
In customer relations, it wasn't unheard of to deal with a down graded passenger because of flight crew rest. I remember dealing with a pax (High Value Gold Card) downgraded from FIRST to Club World because one FIRST seat was needed for flight crew rest. Very difficult to explain to the pax, especially when CW had about 30 spare seats on this flight but I guess it's in the agreement.