I’ve looked into this. It appears to be a minor issue related to polypaint, the specific type of geometry generated by the Snapshot 3d feature, and the Make Boolean Mesh function.
Those multicolored areas are just a bit of misplaced polypaint from the Make Boolean process. If you toggle off polypaint for the resulting UMesh tool it will disappear. You can clear it entirely by filling the tool with a new color by making sure RGB is active with 100% RGB intensity, and using Color>Fill Layer.
You can prevent it from happening by either:
Toggling off polypaint for the cube (paintbrush icon on the cube’s Subtool entry) before using “Make Boolean Mesh”.
Remeshing the resulting Snapshot3d subtool with Dynamesh or ZRemesher prior to performing “Make Boolean mesh”. I’m not certain if it’s the long, stretched polygons or something else not apparent about the Snapshot meshes, but changing the topology prevents the issue. Inserting even a single edge loop to break those long, thin polygons fixes it.
I’ll poke around with this a little more. Let me know if this doesn’t fix your issue!