The only GCT/OAT trip that I have taken where there was a certified SCUBA opportunity (actually on the trip) was on OAT's Ultimate Australia. From Port Douglas we boarded a high-speed catamaran that went out to the Great Barrier Reef for a day trip and you could do a certified dive there off the boat. The catamaran tied off to a docking platform at the reef. Note: the catamaran day trip was included: however, if you opted to do the certified dive it cost extra, etc.
Unfortunately i had a bad cold that day and didn't get to dive. Probably my biggest disappointment of all the GCT/OAT trips that I have taken.
FWIW, here is the outfit that they used: