Hey @wpragnell !
There is no setting to change this since づ (du) and ず (zu) are different letters!
It has been standardized to use ‘du’ and ‘zu’ on the Japanese keyboard to differentiate between ず and づ because they are pronounced the same, but they are different letters.
When wikipedia states that ‘zu’ is the romanization for づ, it is talking about the Hepburn romanization. This is different from JIS X 4063:2000 which is the standardized method for converting keystrokes to kana. The difference between the two is that JIS X 4063:2000 is not meant for romanization, but simply a input method.
What this means is that to type ぬまづ, you have to type ‘numadu’, but if you want to romanize ぬまづ you can use ‘zu’ instead of ‘du’ (Numazu).
Hope this answers your question!