ALT OVERSHOT ON DESCENT WHEN CHANGE IN MAINTAIN ALT MISSED BY THE PF.

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DSNDING INTO LGA WITH VECTORS I RANG 3 BELLS (COMPANY PROC TO SIGNAL 10000' TO F/A'S) JUST AS THE SENIOR F/A WALKED INTO THE COCKPIT. WE WERE STILL SEVERAL MILES OUT SO THE CAPT LET HER STAY IN THE COCKPIT. I WAS GIVEN A CLRNC TO PROCEED TO THE LGA VOR AND WAS DSNDING THROUGH 5000' TO MY ASSIGNED ALT OF 4000'. THE CAPT DISCONTINUED HIS RUNNING COMMENTARY OF THE SIGHTS TO THE F/A TO STATE THAT WE WERE ONLY CLRED TO 6000'. APPARENTLY THE 4000' RESTRICTION HAD BEEN CHANGED TO 6000' WHEN I WAS CLRED TO THE VOR. THE AUTOPLT WAS BEING USED. ON ALL OTHER COMPANY ACFT; THE PNF SETS THE ALT ALERTER (BY PROC) ON THE FMC; IT IS A VERY GRAY AREA. APPROX 70% OF THE TIME WHEN THE AUTOPLT IS COUPLED; THE PF SETS IN ALT CHANGES. THE OTHER 30%; THE PLT ON THE RADIO SETS IT IN. FOR THE NEXT 2 DAYS WE HAD THE PNF SET IN ALL ALT CHANGES. THERE WAS SOME INCONVENIENCE; BUT IT WORKED OUT WELL. THE F/A SHOULD HAVE BEEN ASKED TO LEAVE SHORTLY AFTER COMING UP TO THE COCKPIT. ALSO; APCH CTL SAID; 'THERE WAS NO PROB;' AND GAVE US A NEW VECTOR AND ALT OF 3000'.