There both the same thing if you think about it. There both putting restriction on the chain/motor in the same direction. Neither is bad for the chain. As for the hydraulic motor maybe a minimal effect that will have nothing to due with its lifespan.
IMO any damage is minimal and any difference less so. There may be more of an "Impact" Factor If there is space between the tire and roller when they reverse.
If it is done hundreds of times, the state with the brakes applied will cause greater damage, but if it is done only a few times, the difference is negligible.
Regardless of what we do as operators, this is going to happen. Fortunately, most conveyors are Hydraulic drive which has more "give " plus the chain tensioning spring or air cylinders also cushion.
I don't know what degree of worse it would be but if there is space between the tire and roller - driving over the roller forward or bckward has a certain "Impact" aspect as opposed to the constant tension of having it pass under a stopped car.