At Sikorsky, a TP is assigned by the Chief Pilot to the design team at the outset, and he/she represents the customer operationally. Similarly, a Customer Service rep is assigned to represent the future maintainer. Generally, the TP must sign off on design features that affect the pilot, as well as top-level systems logic and cockpit design.
Your observation about the horizontal stab position is bang on. The pilots were not happy with the nose-up at low speeds and so a major redesign was undertaken, as well as a flight test program to place the tail (I understand that NO helicopter has gone into production with the same tail it first flew, at least not in the last 20 or so years!) At Sikorsky, the TP's are all engineers, and pretty savvy technically and politically, so there is good give and take to get things done right without major head-butting (but sometimes....!)
I worked on the design teams for about a dozen helos, and it was always interesting. For several models, I was the PDT leader for a section of the aircraft, so the pilot's inputs were always strongly considered! The same is true of the Black Hawk and Comanche, where the pilots had strong say.
I can't say what other manufacturers do about their pilot's opinions, we should let them post to tell us.