The new system for upgrading the coastal centers of trade from the DLC clashes with your system of stating provinces. The province which the center lies in has to be a part of a state for you to be able to upgrade it. At the same time in this mod, all the provinces in the entire area that contains the province with the center must be yours and (most realistically) your primary culture before you can state it.

In vanilla, you can state a single province so it is balanced around the number of states you can have and how you want to place them. But you do at least have that choice. It is very important for trade focused nations such as the merchant republics. Playing tall comes to mind as well.

The DLC also had a focus on not having to take all/most the provinces in a trade zone for you to be an effective trader. Instead, taking key locations such as centers and sometimes spending a state to upgrade a center is a viable strategy.

I know you are not supposed to have all the coastal centers of trade upgraded but the system at the moment severely limits you to first conquering an entire area and then forcing your primary culture upon it just to be able to upgrade a single provinces center.

Upgrading coastal centers of trade is already restricted in vanilla and the mod just makes it even more so. Still, there are some valid arguments why it is both too easy and hard already to upgrade them in vanilla.

I don't know what the best solution would be though.