[abenedik]

The MeshBooleanOperations.Subtract method that takes two MeshGeometry3D objects does not take the Transform3D as a parameter (Transform3D is only available when the first parameter is GeometryModel3D, Model3D or ModelVisual3D).

So you need to manually transform the mesh before the Subtract:

Code:

var transformedMesh =  Ab3d.Utilities.MeshUtils.TransformMeshGeometry3D(boxMesh, transform, transformNormals: false);

var subtractedMesh1 = Ab3d.Utilities.MeshBooleanOperations.Subtract(transformedMesh, combinedMesh, translateTransform3D, processOnlyIntersectingTriangles: true, generateInnerTriangles: generateInnerTriangles);

Similar code (calling MeshUtils.TransformMeshGeometry3D) is also part of the Subtract method that take Transform3D as a parameter.