To be honest, I'm not really sure. It's just (to me, anyway) that those racks were probably designed to behave a certain way in case of a catastrophic failure/accident/collision, either in use or not. By locking a bike to the rack, it might (couldn't it?) affect the parameters of the design should such an event happen.
Mind I'm no engineer, nor am I a lawyer, but the transit companies wouldn't have bothered installing those racks if they couldn't have somehow limited their liability.