A321 CAPT EXPRESSED CONCERN REGARDING ATC AND RAMP CTL TAXIING COORDINATION AND QUESTIONED USE OF AMASS DATA AT PHL.

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LANDED RWY 9R. WE WERE THE #2 ACFT HOLDING SHORT OF RWY 9L AT TXWY N. BOTH ACFT CLRED TO CROSS AND CONTACT RAMP AT SPOT 8. ACFT AHEAD STOPPED SHORT OF SPOT 8; TURNED L ON TXWY K TO GO TO SPOT 7. THIS LEFT ABOUT HALF OF OUR ACFT ON THE RWY SIDE OF THE HOLD BARS WITH NO WAY TO MANEUVER CLR OF THE RWY. TWR ON RWY 9L CLRED A COMPANY ACFT TO DEP. WE SWITCHED BACK TO THE CTLR; WHO CLRED US ACROSS AND ADVISED HIM WE WERE NOT CLR OF RWY 9L. HE ACKNOWLEDGED OUR TRANSMISSION; BUT THE COMPANY ACFT CONTINUED ITS TKOF. I CONTACTED THE TWR SUPERVISOR ON ARR AT THE GATE AND FOLLOWED UP WITH THE TWR QA MANAGER THE NEXT DAY. THE MANAGER REVIEWED THE TAPES; ASDE AND AMASS DATA AND CONFIRMED WE WERE CLR OF THE RWY; DESPITE WHAT THE MARKINGS ON THE GND SHOWED. THIS PARTICULAR LOCATION SEEMS TO BE AN ACCIDENT WAITING TO HAPPEN. I'VE BEEN IN THE SAME SIT IN THE L SEAT; JUMPSEAT; AND IN THE CABIN. WE ARE CAUGHT BETWEEN 2 LOCAL CTLRS; GND; AND RAMP. THIS SIT NEEDS TO BE RESOLVED. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: THE RPTR STATED THAT THE LOCAL CTLR HANDLING RWY 9R ARRIVALS ISSUED A RWY 9L CROSSING CLRNC AND INSTRUCTED HIM TO CONTACT RAMP CTL. AFTER CROSSING RWY 9L; THE PRECEDING ACFT; ALSO TRYING TO CONTACT RAMP CTL; SLOWED/STOPPED; PREVENTING THE RPTR FROM CLEARING RWY 9L. THE RPTR SAID HE WENT BACK TO THE LOCAL CTLR WHO ISSUED THE CROSSING CLRNC; ADVISED HIS ACFT WAS NOT CLR OF RWY 9L; BUT A TKOF CLRNC WAS STILL ISSUED FOR A RWY 9L DEP. THE RPTR STATED ATC BLAMES RAMP CTL AND RAMP CTL SITE PERSONNEL TURNOVER AS PROB AREAS. THE RPTR ALSO QUESTIONED THE AMASS PROGRAMMED 'CLR AREA' VS THE HOLD LINES ON THE TXWY POSSIBLY GIVING ATC AND FLC'S DIFFERING CONCEPTS AS TO ACTUAL RWY CLRNC.