I cannot find the reason not to override the autobrakes but my guess is that the auto system is going to be evenly applied on both sides and more controlled. But then I have read some that would say manual is better than auto and so I will not go down that road sir..
Time for me to read that Airbus Journal and do some swotting...
If footbrake pressure exceeds a pre-determined value the autobrakes are disconnected and manual braking is restored with full anti-skid protection.
TW