Duct work sizing question (new home construction)

I apologize if this thread is in the wrong location as I am new to trying out this forum. I’m looking to see if I can get some clarity on some duct work sizing in some of my new home construction houses. Recently I have been going back and forth on proper way to size the main trunk lines. For instance we have had furnaces and A/C units that a third party has ran a manual J load and claims the house needs a 60,000 btu furnace and a 2 ton A/C. This home builder requires 2 vents in every room that shares two exterior walls in their contract. So sometimes we can have a system with anywhere from 20-27 heat runs total. Which if ran as 6” runs is around 80-100 cfm. Which equals out to 2,000-2700 cfm on the supply side. My question to everyone would be do I size my main trunk line based on how many heat runs I have or should I stick to sizing it based off equipment size? I guess my concern would be having the duct work oversized for the equipment being installed.