COMMUTER TAXIES ONTO RWY TO BACK TAXI THINKING CLRED. SECOND ACFT MUST GAR.

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RECEIVED CLRNC TO TAXI FROM GND CTL AND PROCEEDED TO TAXI TO RWY 36. WE PROCEEDED TO TAXI VIA THE RAMP; TAXIWAY E AND RWY 29. UPON LEAVING RWY 29 AND HOLDING AT ITS END/INTXN WITH RWY 36; I HEARD THE TWR REQUEST AN ACFT TO EXECUTE A GAR AND ENTER A R DOWNWIND FOR RWY 36. IT WAS AT THAT TIME THAT THE COPLT TURNED TO ME AND ASKED IF I DIDN'T FEEL IT WAS NECESSARY TO HOLD AT RWY 29. APPARENTLY THE COPLT HAD UNDERSTOOD FROM GND THAT WE WERE TO HOLD SHORT OF RWY 29. I HAD MISUNDERSTOOD THE CLRNC AND ASSUMED WE WERE TO TAXI ALL THE WAY TO RWY 36. WE HAD HAD SEVERAL FLTS DURING THE PREVIOUS 24 HRS AND HAD BEEN CLRED BY GND ALL THE WAY TO RWY 36 ON EACH PRIOR TKOF. NEITHER CREW MEMBER HAD SEEN THE TFC WHICH APPARENTLY HAD BEEN LINED UP FOR LNDG ON RWY 29; AND SUBSEQUENTLY INITIATED A GAR. WHEN I ASKED WHY THE COPLT DID NOT STOP ME AT ANY TIME DURING MY TAXI INCURSION FROM TAXIWAY E ONTO RWY 29 AND THEN UPON HOLDING AT 36; HE INDICATED HE HAD BEEN PREOCCUPIED WITH HIS PREFLT DUTIES AND HAD HIS HEAD DOWN THE ENTIRE TIME AND HAD NOT REALIZED WHERE WE WERE. I WAS SURPRISED THAT THE CTLR DID NOT CHASTISE ME AT THE TIME; AS WE HAD NO OFFICIAL RECOGNITION THAT OUR INADVERTENT TAXI HAD RESULTED IN THE GAR. IN FACT THE NEXT RADIO CALL WAS FROM THE TWR ADVISING US TO TAXI INTO POS AND HOLD ON RWY 36. SO; IT MAY BE CONJECTURE; BASED ON THE COPLT'S UNDERSTANDING THAT WE HAD CAUSED THE GAR BY TAXIING THROUGH RWY 29. AS PIC I UNDERSTAND MY RESPONSIBILITIES; I BELIEVE THE PROBLEM RESULTED FROM MY INITIAL MISUNDERSTANDING OF THE TAXI CLRNC; THE COPLT'S INCOMPLETE READBACK OF THE TAXI CLRNC; THE COPLT'S PREOCCUPATION WITH PREFLT CHKLISTS AND A PARTIALLY CONFUSING INTERPLAY OF GND/CTL AND TWR AUTHORITY AT BETHEL. I RECOGNIZE THAT GND CAN INITIATE AND AUTHORIZE ITS TAXI CLRNCS AS IT SEES FIT WHICH INCLUDES AUTHORIZATION TO TAXI THROUGH; ACROSS OR PAST ACTIVE RWYS AND SUCH CLRNC NORMALLY AIDES IN THE FLOW OF EFFICIENT TFC HANDLING. I DO BELIEVE IT INAPPROPRIATE THAT A GND CTLR ARBITRARILY ALLOWS TFC ONTO AN EXISTING; USABLE RWY OR REQUIRES TWR FREQ WHENEVER XING A RWY. IN ANY EVENT IT WOULD HELP IF EVERY ARPT HAD A POLICY OF GND ONLY OR TWR ONLY OF AUTHORIZING RWY XINGS. IF THE CTLRS CHANGE THEIR RESPECTIVE AUTHORITIES ON A WHIM; EVEN PLTS FAMILIAR WITH THE LCL OPERATING RULES WILL OCCASIONALLY GET CONFUSED OR CAUGHT UP IN A SITUATION LIKE THIS ONE. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING INFO: RPTR STATES HE BELIEVES BIGGEST PROBLEM IS HABIT AT THIS ARPT OF GND CLRING ACFT ONTO A RWY. HE HAS NEVER EXPERIENCED THIS ANYWHERE ELSE. WILL ALWAYS STOP TO CONFIRM BEFORE ANY ENTRY FROM NOW ON. FAA HAS CONTACTED COMPANY BUT HAD A PROBLEM WITH CLOCK THAT DAY AND DO NOT KNOW WHICH FLT WAS REALLY INVOLVED. RPTR HAS NOT HEARD THE TAPE AND DOESN'T KNOW IF 'HOLD SHORT' INSTRUCTIONS WERE ISSUED.