PIC ELECTS TO NOT FOLLOW THE MANDATES OF TIME REQUIRED BY BRAKE ENERGY CHARTS AFTER A REJECTED TKOF AND SUFFERS DEFLATED TIRES ON LNDG AT DEST ARPT.

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FOLLOWING ABORT AT DFW DUE TO AN AUTOPACK TRIP FAIL TO ARM CREW CONSULTED BRAKE COOLING CHART. MAX SPD ACCELERATED TO WAS 100 KTS WHICH REQUIRED 42 MIN COOLING TIME. HOWEVER; ACFT WAS ALLOWED TO ROLL OUT TO THE END OF THE RWY WITH LITTLE BRAKING. CAPT DECIDED TO USE 10 MIN OF COOLING AND LEAVE GEAR DOWN FOR 1 ADDITIONAL MIN DUE TO THE SMALL AMOUNT OF BRAKING USED. (42 MINS NOT USED SINCE ACFT WAS NOT STOPPED FROM 100 KTS DUE TO BRAKING. ROLLOUT WAS PRIMARILY USED WITH ONLY LIMITED BRAKING WHICH CORRESPONDS TO A 75 KT BRAKE APPLICATION ON THE CHART.) ON LNDG BOTH TIRES ON THE R MAIN GEAR WERE FLAT. THERE WAS MINOR DAMAGE TO R INBOARD FLAPS AND FLAP FARING AND WHEEL RIM. THERE WERE NO INJURIES BUT THE RWY AT MIA WAS TEMPORARILY CLOSED. MAINT RPTED EVIDENCE THAT TIRES DEFLATED WHILE IN WHEEL WELL. I BELIEVE BRAKE COOLING CHARTS SHOULD BE CHANGED TO REFLECT ENTERING THE CHART WITH THE MAX SPD ATTAINED AND NOT THE BRAKE APPLICATION SPD. CURRENT TRAINING AND PERCEPTIONS ARE THAT THE CHART IS FOR THE AMOUNT OF BRAKING APPLIED; NOT SLOWING FROM A MAX SPD.