Merchants and Foundries are working mostly as intended I think. The number of merchants you can have is equal to the number of Trading Post buildings you have, up to 9 (equal to the three traders, three camels, and three ships from previous patches). If you have less cities than that, certain techs and leader traits increase the limit, as detailed in the Trade section of the PAE Concepts part of the Civilopedia.
For the bronze foundries, each one now requires you to have one copper, and one tin/lead. So you'll have to build them strategically as you acquire the resources to do so, as opposed to putting one down in every settlement in your empire.
One question that I have about the new version: In the PAE Concepts section on supply, it now mentions that the player's maximum units per stack are 10/15/20... But it doesn't seem to say anything about what causes this limit to increase, so I don't really have any idea when it's safe to add more units to my stacks.
Also, the goldsmith building still shows up in cities that can't keep it, though the similar problem with tanneries seems to have been fixed!