PLT OF SMA ACFT MADE TKOF AND LNDG ON A CLOSED FLOODED RWY ON AN ARPT WITH AN OPERATING CTL TWR.

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MY FIRST FLT OF THE DAY WAS CANCELLED DUE TO RWY CLOSURE. ACFT WERE OBSERVED TAKING OFF AND LNDG SO I CALLED PALO ALTO TWR ON THE PHONE. THEY STATED THAT ACFT WERE BEING ALLOWED TO TAKE OFF AND LAND AT THEIR OWN RISK. I VISITED THE TWR IN PERSON; SPOKE TO BOTH ATC SPECIALISTS AND WATCHED OTHER ACFT DEPART AT THEIR OWN RISK. THEY HAD THE APPROPRIATE SECTION IN THE HANDBOOK HIGHLIGHTED AND SAW NO PROB WITH ACFT OPS AS LONG AS IT WAS CLR ON THE TAPE THAT OPS WERE AT THE PLT'S OWN RISK. AT APPROX AM00 PST I DEPARTED AT MY OWN RISK FOR A LCL PHOTO FLT. AFTER DEP I RECEIVED PERMISSION TO TRANSITION THE ATA FROM A R XWIND DEP. AT APPROX AM30 PST I RECEIVED PERMISSION TO TRANSITION THE ATA FROM THE NE TO THE SW. AT APPROX PM00 PST I RPTED APPROX 6 MI TO THE S FOR LNDG AT MY OWN RISK AND WAS TOLD TO ENTER ON THE L DOWNWIND. THERE WAS NEVER A HAZARD AND THE LNDG WAS UNEVENTFUL. LATER IN THE DAY I WAS TOLD THE SAN JOSE FSDO WAS ENRAGED AT WHICH WAS OCCURRING AND HAD PLANS TO PROSECUTE UNDER FAR 91.129(H). IN LIGHT OF MY DISCUSSION WITH THE TWR SUPVR I FELT THAT MY OPS ARE EXEMPT DUE TO FAR 91.129(A) 'UNLESS OTHERWISE AUTHORIZED.'