ACR-SMT TOOK OFF WHLE ACR-WDB WAS CROSSING RWY AT NIGHT.

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WDB X WAS CLRED FOR A VISUAL APCH TO RWY 22L AT BOS AT APPROX XA00 LCL TIME. THE LNDG AND ROLLOUT WERE NORMAL. WE TURNED OFF THE RWY ON ECHO TXWY. AT THAT TIME THE TWR CTLR ADVISED 'CROSS THE RIGHT SIDE AND TAXI TO THE GATE ON THE INNER; STAY WITH ME.' AS THE ACFT APCH RWY 22R BOTH THE F/O AND I LOOKED TO THE RIGHT TO CHK THE DEP END OF RWY 22R AND ALSO CHK FOR TFC THAT MIGHT BE LNDG ON THAT RWY. AS NO TFC WAS SEEN; WE CONTINUED TO CROSS RWY 22R. AT THAT POINT LNDG LIGHTS WERE TURNED ON BY AN ACFT ON RWY 22R. THIS ACFT DEPARTED RWY 22R FROM AN INTXN AT MIDFIELD AND PASSED APPROX 100-150' OVER THE TOP OF MY ACFT AS WE XED RWY 22R. WE REACHED THE GATE AND I CALLED THE TWR. IT SEEMS THAT THE ATC TWR POS WAS WORKING GND CTL; TWR AND I THINK CLRNC. THE GENTLEMAN I TALKED TO SAID THAT I HAD BEEN CLR TO CROSS; AND THE OTHER ACFT HAD BEEN CLRED FOR POS AND HOLD 22R AT CHARLIE. I DON'T KNOW IF THIS ACFT TOOK OFF W/O CLRNC; OR THE TWR CTLR LOST HIS MENTAL PICTURE AND FORGOT THAT WE WERE XING THE RWY. WHAT BOTHERS ME THE MOST IS THE FACT THAT WE HAD MORE CONFUSION AND MIX UPS AT BOS LOGAN THAN ANY OTHER ATC FAC IN THE US. I DON'T KNOW IF THEY ARE SHORTSTAFFED; UNDERTRAINED OF IF THE NOISE ABATEMENT ROUTES PUT TOO HIGH A BURDEN ON THE SYS. WHEN DISCUSSING THIS INCIDENT WITH SEVERAL OTHER CREWS; WE ALL AGREE THAT BOS IS SETTING ITSELF UP FOR A MAJOR ACCIDENT. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING: CAPT WAS CALLED AND HE ADVISED THAT EVEN THOUGH HE TELEPHONED THE TWR AFTER REACHING THE GATE; HE WAS UNABLE TO ASCERTAIN WHETHER THE PLT OF THE OTHER ACFT HAD TAKEN OFF WITHOUT CLRNC; OR THE CTLR HAD ERRED IN ALLOWING THE TKOF WHILE HE WAS XING THE RWY. HE SAID THAT THE PERSON HE TALKED TO IN THE TWR CAB WAS APPARENTLY ALONE; BECAUSE WHILE THEY WERE TALKING HE COULD HEAR THE PERSON TALKING ON THE RADIO AT THE SAME TIME. CAPT ALSO SAID THAT THIS SAME TYPE OF INCIDENT HAD HAPPENED TO THEM ABOUT 2 MONTHS BEFORE AT BOS.