The whole subject of unification got very muddled, and I lived through it, because the administrative issues such as removal of duplication and inefficiencies of scale became confused with operational matters. Thus strange things happened such as the reduction of the number of trades to less than one hundred because Mr Hellyer stated that as one of the goals of his grand design. People in the support world generally came out of this much the worse for wear, as opposed to say the combat arms who were screwed about to a much lesser extent.
When the commands were unified, which was the second major step after the creation of Canadian Forces Headquarters, Maritime Command absorbed the RCAF maritime patrol world and Mobile Command took over what little tactical fast air we had, a few T33s at Rivers, I believe. The army at that time already had integral aviation including 1 Transport Helicopter Platoon with six (I think) Voyaguer helicopters. The old RCAF transport and air defence commands remained relatively intact and Air Training Command became the nucleus of Training Command which absorbed the other services' schools.
Mobile Command was very roughly based on the Fleet Marine Force and consisted of the land forces in Canada, including the aviation assets, the tactical air squadrons and the Buffalo squadron which was being formed at roughly the same time. It was planned to have a mobile logistics tail as was the case for the Marines, but force reductions soon ended that.
The forces in Europe, Canadian Army National Force Europe and the 1st Air Division, remained as two separate commands reporting to CFHQ at this time.
The reserves did not belong to any of the operational commands, but were part of a separate chain which did all sorts of harm.
Where the "jointness" fell down, and this was never resolved, was that the existing operational roles were single service. For example Maritime Command including Maritime Air Group had a very real and very necessary operational role under the Supreme Allied Commander Atlantic. Mr Hellyer liked to complain that the services all had different concept of operations with the navy seeing itself escorting convoys, the army fighting a 30-day land battle in Europe and the air force going out in a blaze of nuclear energy. All this was quite true, and it was precisely because these were the roles of each service in a period of escalating tension leading to the outbreak of conventional war in Europe that could go nuclear at any time.
It was very difficult to become joint under these conditions which really remained until the end of the Cold War. Today we (or rather you) are in a whole new game and logic seems to indicate that jointness is the way ahead, at least until something completely unforeseen comes along again.
