to get a value for IfcAxis2Placement3D.Axis, you can simply apply the given rotation to vector (0,0,1) or (0,0,z) with any real value z (any other not-normalized z-axis vector). Likewise, to get a value for IfcAxis2Placement3D.RefDirection, apply the given rotation to vector (1,0,0) or (x,0,0) with any real value x (any other x-axis vector) . You could also use any other vector in the xz-plane as Refdirection, but one that is orthogonal to the z-axis is just fine. It is just meant to fix the rotation about the z axis once you have the z-axis itself fixed via the Axis attribute.
Hope that helps,
Scaling is risky… Because it may impact many other things. Are you expecting the scaling to also impact dependent objects (parts)? Are quantities for that object recalculated based on scaled geometry? Are any dimension parameters scaled as well?
So I would be really, really careful before introducing scaling and if you can avoid it (e.g. by parametrically controlled size/dimension), than you don’t need scaling at all.