After some more tinkering, I figured it out. In order to have custom supports to be placed on the model (as well as on the build plate) I had to have the support setting set to Everywhere. The missing supports showed up after this.
In the end, this didn't produce the desired result as I didn't want supports inside the model. So I ended up enabling supports "Everywhere" and then using the support blocker instead to prevent supports inside the model.
Hope this helps someone else.