1965 was the last year that all heavy production got the spigotted cylinder, 500cc, 650cc and 750cc.
I have heard of re-drilling and tapping the Atlas cylinders with the 5/16 head bolts to take the 3/8" Commando head bolts, but if you look between the fins on both an Atlas and 750cc Commando cylinder you will see that the Commando cylinder had a lot of material added in there for the bigger head bolts to anchor in, the Atlas was pretty skimpy in this area.
The 500cc and 650cc engines had the 3/8" bolts just like the Commando, it was just the Atlas that had the small diameter head bolts.
It was a neat trick they did to convert the 650 to a 750, all they did was make a new cylinder and pistons and did some different machining on the 650 crankcase and head castings, some re-balancing of the crank and there you were. It was sort of a turd of an engine though, with more vibration and low compression and initially a single carb, it was supposed to be a docile touring bike with a broad spread of power, the same idea Norton had again later for the 850.
I have 1962 Atlas engine shop #2 which I want to restore someday and at least put on a stand.