I currently have a 18 y.o. 80K btu 92% efficent trane upstairs. It is for 1500 sq ft. It short cycles (like my bedroom system)---comes on for 5 minutes, temp goes up 2 degrees and goes off. The duct is in a well ventilated antic, and is r4? ductboard.

I'm in the process of replacing it. And minor duct work. The load calc supposedly was 56k, (which I think is high for above average 1995 construction)

I was quoted a trane modulating “affinity” 60k unit. I've read briefly that the the long slow gentle heating isn't ideal for attic placed ductwork. Heat loss in the ducts. I'm wondering just how variable are the york modulating systems---could I set it to run in 10 minute cycles only, or even 5 minute cycles.
What is the current preferred way to trade off comfort and shorter runs for efficiency? Stay with a single stage?