Like all examples of cross cockpit gradient or CRM, the AAC have both good and bad. Generally it falls into 2 very distinct domains - flying duties, and the other stuff. When conducting flying duties the Aircraft Commander is the Aircraft Commander; period. It is an appointment, not a rank, so be it a Sergeant, a Warrant Officer, a Major, or anything in between, those individuals conduct themselves as the crew of an aircraft would be expected to. There are many examples of SNCO's in command of Officers for Flying duties, particularly on the QHI stream, where they have the additionally responsibility of flying standardization within the unit. Back on the ground, the individual will assume secondary duties commensurate with their rank and expect the normal military courtesies to be observed between the ranks.
There will always be cases where some young SNCO gets a rush of blood to the head over the chance to be in "charge" of an officer while in the cockpit, just as there are some young officers who feel a tad resentful of being commanded by an old crusty SNCO, but it is very quickly recognized and resolved. Some well documented falling out in the cockpit (the Kegworth twins) have been entirely due to the unsuitability of the individual from a CRM viewpoint, which may have been exacerbated by the rank gradient, but was not because of it.
It is a well tried and tested opportunity to allow experience and command to embrace each other in a taxing, but mutually respectful environment. The AAC should be rightfully proud of the way they have executed this system, but it is also noteworthy, as an earlier poster mentioned, that the best of RAF history and reputation was founded on Officer and SNCO pilots working together.