You are missing an understanding of local goods production in EU4.
Manufactories increases local goods production by +100%.
Local goods production is instrumental not only to your production income, but also to the trade value generated by the province. Furthermore, it is instrumental to getting the most manpower out of a province, as the base manpower part of your provincial manpower (i.e. the part that is not affected by constants like the +25 and +50 from army buildings) is linearly dependent on your base manpower factor, which itself is determined by the goods production.
The result is that manufactories are the most
monarch-point efficient ways of boosting your direct income, trade, and manpower by buildings in most cases, and it does all three of them at once for a mere 10 monarch points. It is
not always the most
ducat efficient way, so the question you have to ask yourself is what is important to your country in the situation you are in. Money or monarch points? And how much do you feel you need all the benefits the manufactory brings in compared to a more specialized approach?
For countries with a hefty income spamming manufactories is the order of the day, as they typically have much better access to money than monarch points and have so many things to spend monarch points on.