B727 CREW LNDG AT BOS AVOIDS POSSIBLE COLLISION AT INTERSECTING RWYS.

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ILS RWY 4R BOS; ATIS RPTING 7 SCATTERED AND GOOD VISIBILITY. IOE FO FLYING; CAPT CHK AIRMAN IN COMMAND. NORMAL APCH; BUT SURPRISINGLY DID NOT SEE RWY UNTIL DECISION HT (200 FT AGL) IN POOR VISIBILITY/MIST. FO MADE LNDG WITH SOME VERBAL AND MANUAL ASSISTANCE FROM CAPT. AT TOUCHDOWN; HEARD 'GO AROUND IF ABLE.' WITH SPD BRAKES AND REVERSERS DEPLOYED; NEAR MAX GROSS WT LNDG; AND UNAWARE OF PROB; I SAID 'UNABLE;' AND AGGRESSIVELY STOPPED ACFT; ONLY THEN SEEING B727 XING FROM 11 - 1 O'CLOCK POS ON RWY 15R; APPARENTLY UNDER HVY BRAKING. UPON INQUIRY TO TWR; WAS ASKED TO CALL ON TELEPHONE; AS WAS THE OTHER CAPT. TWR SUPVR; APOLOGIZED AND STATED THAT INVESTIGATION OF CTLR'S ERROR WAS UNDER WAY; AND WE EXCHANGED INFO. HE SAID WHEN WE 'POPPED OUT' AT 200 FT; THE TWR CTLR REALIZED THE CONFLICT AND ORDERED ME TO GO AROUND. (MY SO INFORMED ME AFTERWARD THAT HE DID HEAR A GAR ORDER 'IN THE FLARE;' BUT I DID NOT POSSIBLY DUE TO THE VERBAL AND MANUAL ASSISTANCE BEING GIVEN TO THE IOE FO.) AT SOME POINT; SHE APPARENTLY ORDERED THE OTHER B727 TO ABORT TKOF AT HIGH SPD; ON A DIFFERENT FREQ. I STOPPED PRIOR TO THE INTXN; HE DID NOT. VISIBILITY WAS POOR; BUT ESTIMATED SEPARATION WAS 500-1000 FT. I BELIEVE IN RETROSPECT THAT IF I HAD HEARD THE ORIGINAL GAR ORDER AND COMPLIED; CONSIDERING WT; PERFORMANCE; AND TIMING; THE TOTAL SEPARATION WOULD HAVE BEEN EVEN LESS; ALTHOUGH SOME OF IT VERT. IF THE OTHER B727 HAD CONTINUED TKOF; AND WE DID GAR; A VERY NEAR MISS WAS LIKELY AT BEST. ALL THIS IN RETROSPECT; OF COURSE.