Why doesn't the Army have enlisted helo pilots?

The Army Air Corp had Flying Sergeants during WWII, but phased them out. A good part of the Warrant program is to allow that enlisted person to say in a flight position, something that doesn't happen with Commissioned Officer, while increasing their pay and giving them some status inside the system.

Don't have an answer for your question, but the information you cite concerning a junior being in command of a vessel is not that unusual. The same thing happens in aircraft and who is scheduled as the pilot in command is decided by who the squadron commander has assigned as the aircraft commander. Qualifications often has nothing to do with it.
I, as a 1st Lt in VN, was assigned as the aircraft commander with my copilot being a Major General. All though I was well qualified, the general had flown helicopters in Korea, then went on to be one of the principles in the development of the model aircraft we were flying. I was good, but I'll bet the General could have shown me a few things, but since he was not in the chain of command for my unit, it was my aircraft and I called the shots.

In my early days at NAS North Island there was a CPO Pilot in squadron VRF 31 on the East Coast. He would often land at NAS North Island delivering an Aircraft for VN service (1965). As a very senior Pilot he was usually in command & being about the only enlisted pilot left was always outranked by his Co-Pilot. Can not imagine any Officer working with him trying to use rank. It is a matter of competence, leadership & presence.