I don’t know if this is still an open question, but posting an answer for whoever else is looking.
To set the internal material, open the Geometry Collection and add a new material to the Materials array. Save the Geometry Collection.
Then when you are in the Chaos Fracture settings window, scroll down to Materials and set the Internal Material to be the material you added earlier.
Make sure to set it in the fracture window. It has some defaults and/or legacy behavior to try to figure out what is inside or outside if you don’t specify, but this can get strange.
I’m still working through this as well, so there could easily be other steps/ways to do it.
Hope that helps.