A C560XL FLC STARTS THEIR TURN ON COURSE DIRECT TO SAC BEFORE REACHING THE SGD VOR LOCATED 5 MI SW OF APC; CA.

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JUN/TUE/00; APPROX XA30 AM PDT; CITATION 560XL. DEPARTING: NAPA VALLEY; CA (APC) ENRTE BUTTE; MONTANA (BTM). CLRNC RECEIVED WAS SLIGHTLY DIFFERENT FROM THE FLT PLAN THAT HAD BEEN FILED. THE CLRNC RECEIVED AND ACKNOWLEDGED WAS: 'AFTER TKOF DIRECT TO SKAGGS ISLAND; DIRECT SACRAMENTO; DIRECT TO MUSTANG; BATTLE MOUNTAIN; HIA; DIRECT. MAINTAIN 8000 FT; EXPECT FL370 IN 10 MINS; DEP CTL 127.8; SQUAWK XXXX.' THE REVISED ROUTING APC TO (SGD-SAC-FMG-BAM-HIA) BTM WAS PROGRAMMED INTO THE FMS'S. WX WAS CLR WITH GOOD VISIBILITY. WE WERE THEN CLRED FOR TKOF ON RWY 18R AND WHEN AIRBORNE INSTRUCTED TO CONTACT DEP CTL; WHICH WE DID. ACCORDING TO THE FMS; SKAGGS ISLAND VOR IS 229 DEGS; 4.8 NM FROM APC. AFTER TKOF WE WERE IN A SHALLOW R TURN TOWARDS SGD; CLBING AND ACCELERATING. THE BANK ANGLE WAS SHALLOW BECAUSE WE WERE LOOKING FOR THE SINGLE ENG ACFT WE HAD OBSERVED MAKE A R TURN IMMEDIATELY PRIOR TO OUR DEP. OAKLAND DEP CTL THEN ADVISED US OF SOMETHING LIKE 'TFC 12 O'CLOCK POS AND 2 MI; 1000 FT ABOVE YOU;' WHICH I BELIEVE WOULD HAVE BEEN 3000 FT; OR THE TA MAY HAVE STATED 3000 FT; AND WE OBSERVED OUR ALT AS 2000 FT AND CLBING; VIRTUALLY SIMULTANEOUSLY WE RECEIVED A 'TFC ALERT' FROM OUR TCASII.' WE BOTH BEGAN LOOKING OUTSIDE THE ACFT FOR THE TFC CONFLICT. ONCE COMFORTABLE WE WERE ABOVE THE TA ACFT ALT WE RESUMED OUR IN-COCKPIT DUTIES. BOTH FMS DISPLAYS WERE SHOWING THE LEG 'SGD-SAC;' INDICATING TO US THAT WE HAD PASSED THE SGD VOR. WE TURNED L INTENDING TO INTERCEPT THE DISPLAYED COURSE; WHICH WE BELIEVED TO BE IN ACCORDANCE WITH OUR CLRNC. PRIOR TO REACHING THAT INTENDED HEADING OAKLAND DEP BROADCAST 'YOU WERE CLRED TO THE SKAGGS VOR; IT LOOKS LIKE YOU ARE PROCEEDING DIRECT TO SACRAMENTO.' I VAGUELY RECALL SAYING SOMETHING LIKE 'AFFIRMATIVE; WE SHOW WE HAVE PASSED SKAGGS VOR;' TRYING TO EXPLAIN WHAT WE WERE DOING. OAKLAND'S RESPONSE WAS 'IMMEDIATE R TURN DIRECT TO THE SKAGGS VOR.' WHICH WE COMPLIED WITH; RESULTING IN NOT MUCH MORE THAN A 270 DEG TURN DIRECT TO SAC. SHORTLY THEREAFTER; WE WERE ADVISED TO CONTACT THE CTR ONCE WE WERE ON THE GND 'REGARDING A POSSIBLE DEV;' AND HANDED OFF TO THE NEXT CTLR. AFTER LNDG AT BUTTE; MONTANA; WE CALLED THE NUMBER GIVEN AND SPOKE WITH SOMEONE (DID NOT GET A NAME) WHO STATED 'I WAS NOT IN THE ROOM AT THE TIME; BUT I HEARD WHAT HAPPENED...YOU GUYS TOOK OFF AND PROCEEDED DIRECTLY TO THE SACRAMENTO VOR; POSSIBLY VIOLATING MIL APCH'S AIRSPACE... OUR DEP PROC FROM NAPA ARPT IS DIRECT TO SKAGGS VOR THEN SACRAMENTO...' I THEN RELAYED WHAT IS STATED ABOVE AND THE RESPONSE WAS 'OH...WELL...A DEV HAS BEEN FILED AND YOU SHOULD CALL IN A FEW DAYS; AFTER THE QUALITY CTL BOARD HAS HAD A CHANCE TO REVIEW THIS.' I RECOMMEND THAT A STANDARD INST DEP FOR THIS ARPT BE PUBLISHED TO AVOID ANY CONFUSION OF AVOIDANCE OF ANY RESTR MIL AIRSPACE. ALSO; TWR CTLR COULD ADVISE TFC TO BE AWARE OF LCL MIL AIRSPACE. WE ACTED PROPERLY IN THE INTEREST OF TFC AVOIDANCE AND SAFETY OF FLT.