OK, that in mind you are pointed in the direction I would have suggested. Within reason, a shorter reach and higher stack to the bars is more comfortable. But that often is related to strain on the back and neck that can happen with the traditional long/low position aimed at performance and aero, as you noted.
But like anything else, there is a limit to that. I doubt most people would enjoy a super upright townie/cruisier bike fit for training, especially if power is a close 2nd priority.
Outside of that, the saddle comfort related stuff may be worthwhile to consider, broadly speaking.
Ultimately, specifically targeting the discomfort areas you have is essential. Neck, hand, back, bottom and such will likely lead to different directions with a non-aero limit.