I do not know the details about redduck's situation, and am also not an HVAC expert. But I will offer some observations made in my parents' past homes and my own homes. These homes range in age from 1940s, 1950s, 1980s, and my newest home built in 2007.
The earlier homes had all metal ducts. The branch lines going into each room tended to be small, of 8" diameter, I think. I think I have seen 6" also, but am not sure. These older homes were also built before the popularity of the AC.
Newer homes use slinky hoses, but they are bigger, of 10" or even 12" for longer runs. But even the newest home uses a big square rigid metal duct as the main trunk. The AC/heat pump blows into this large duct, from which the flexible hoses fan out to run to each room.
If the airflow to the distant rooms is inadequate, it is reasonable to replace the corresponding duct with one of a larger size. In an older home, that would mean replacing the old smooth round metal duct with a slinky. I do not see that as a big deal. I would prefer to have a larger duct to ensure a good airflow. If too much flow, I can always close down the louvers at the registers.
Perhaps redduck's contractor was talking about upsizing the branch lines to the remote rooms. That would make a lot of sense, else all that extra capacity of the new AC/furnace would be for naught.