System Information
Operating system: Windows 10
Graphics card: Nvidia GTX 1060

Blender Version
Broken: (example: 2.80, edbf15d3c044, master, 2018-11-28, as found on the splash screen) 3.0.0
Worked: (newest version of Blender that worked as expected) N/A (uses node that debuted in 3.0)

Short description of error
When I use the Set Material node on a given piece of geometry and then wire the output into the second input socket of a Mesh Boolean node with the mode set to "Difference", the new geometry generated by the Mesh Boolean node is given whatever material is in the second slot in the object's Material Shelf, rather than reflecting the material specified by the Set Material node.

Exact steps for others to reproduce the error
Based on the default startup or an attached .blend file (as simple as possible).
Create at least two materials in addition to the existing default material on the object. Create a new Geometry Nodes modifier on the object. Insert a Mesh Boolean node onto the existing noodle with the mode set to "Difference." Next, create a Mesh Primitive node (any), and wire the geometry from it through a Set Material node. Specify a material, and it should work fine on the geometry itself. However, if you now wire that into the second input socket of the Mesh Boolean node, you will notice that, regardless of what Material you specify in the Set Material node (as long as you at least specify something), the new geometry that is generated always shows whatever Material is currently in the second slot in the object's Material Shelf. Attached is a demo blend file.