This may be less to do with the ability of the system to brake and more to do with timing.
The autobrake won't kick in until the thrust levers are at idle, which means that for an RTO where the pilot applies maximum brakes simultaneously with closing the thrust levers they gain a fractional head start on the autobrake. I can imagine this being a slower process on the 747 given its age and architecture.
The above is just a guess, admittedly.