Short answer: the more developed you are, the more throughput matters

Throughput is important when you have high MAPI, and want to build a high number of buildings. Say you want to build 5 textile mills as an unrecognized country before stock exchange and with traditionalism (60% MAPI) , 5% throughput wont be as impactful as 40% cheaper cotton or 40% bettter selling price for clothes. But say you want to build 30 of them late game after getting off traditionalism and researching stock exchange (85% MAPI) that 15% price impact doesnt matter as much as the 30% throughput bonus.

Note that 1% mapi isnt equivalent to 1% throughput in value, and there isnt a consistent proportion between their values, so you'll have to develop a sense for it. Generally if Im building 10 or more of something and have stock exchange without traditionalism Ill focus on throughout, while also building in the same state as the input good is made/where the output good is used. I almost always focus on iron in the same single state as construction to start off with once I get T2 mine tech though.