LGT CLRED TO LAND WITH ACFT BEYOND HOLD LINE AT RWY INTXN.

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FLT WAS CLRED TO LAND AT SJU. FLT WAS ALIGNED WITH RWY 10 BUT CLRED TO LAND ON RWY 8 EVEN THOUGH ANOTHER ACFT WAS SLIGHTLY OVER THE HOLD LINE AT TXWY Y. PRIOR TO FINALLY ACCEPTING THE LNDG CLRNC; THE CAPT AND FO MADE REPEATED ATTEMPTS TO OBTAIN LNDG CLRNC FOR RWY 10 BUT THE TWR OPERATOR REFUSED CLRNC TO LAND RWY 10 EVEN THOUGH THE RWY WAS CLR; LONGER; AND THE ONE WE WERE LINED UP ON ANYWAY. LNDG WAS THEREFORE MADE ON RWY 8 AND WAS WITHOUT INCIDENT. IT IS NOT KNOWN TO THIS RPTR WHAT; IF ANY; REASONS THE TWR OPERATOR HAD FOR REFUSING FLT ITS CHOICE OF RWY BUT IT APPEARED TO BE AN ARBITRARY DECISION. LNDG WAS MADE ON RWY 8 WITHOUT INCIDENT BUT LNDG CLRNC FOR THAT RWY SHOULD NOT HAVE BEEN ISSUED OR ACCEPTED DUE TO THE OTHER ACFT BEING OVER THE HOLD LINE. THERE WERE FAST MOVING RAIN SHOWERS CLOSE TO THE ARPT HOWEVER; AND THE ACFT OVER THE LINE DID NOT PRESENT A HAZARD; SO THE CAPT WENT AHEAD AND LANDED; THAT SEEMING TO BE THE BEST AND SAFEST COURSE OF ACTION. IT SHOULD BE NOTED THAT THE OTHER ACFT WAS OVER THE HOLD LINE HAVING BEEN GIVEN AND THEN CANCELED TKOF CLRNC; AND HAD INFORMED THE TWR OPERATOR OF HIS POS. SUPPLEMENTAL INFO FROM ACN 318601: FLT LANDED ON RWY 8 AT SJU WITH OTHER ACFT ACROSS THE HOLD LINE AT TXWY Y. TWR AUTH LNDG. THE TWR OPERATOR SHOULD NOT HAVE AUTH A LNDG TO RWY 8 AND WE SHOULD NOT HAVE ACCEPTED THE RWY ONCE THE OTHER ACFT RPTED THE INCURSION OF THE RWY ENVIRONMENT. NUMEROUS REQUESTS FOR RWY 10 WERE NOT ACCEPTED. FAST MOVING RAIN SHOWERS APCHING THE ARPT FROM THE S RELEVANT FACTOR IN DECIDING TO LAND AND NOT GAR FOR ANOTHER APCH.