Volumetric Subtraction unsupported? Shape::cut() function does not do the same thing as union()

[EnnFour]

I want to make a volumetric subtraction (object B occupies some space in Object A: make Object B into air instead of material).
The Shape::cut() function just gives me a bunch of random looking shapes?
However, when I do the following:

        box = cadquery.Workplane().box(x_mm, y_mm, z_mm, centered=False)
       
        assembly = cadquery.Assembly()
        assembly.add(box, name="box")

        for index, cutout_location in enumerate(cutout_locations):
            cutout = MagazineCutout.create(spec.cutout)
            cutout.loc = cutout_location
            assembly.add(cutout, name=f"cut_{index}", color=cadquery.Color("red"))

        assembly.save("28jan.step")

All the wireframes show that my cutouts are in the correct position.
Modifying the code slightly to use the function box = box.cut(cutout) leaves me with garbage that sorta resembles the shape of the cutout but not quite.

I can't find reference to any other functions which permit volumetric subtraction. Is this not a supported feature?

[adam-urbanczyk]

Bool ops should work. MRE? What is the cutout?