You might get chipping and my experience is that this depends both on how well the aluminum surface was prepared for the adhesion of the coating and on how aggressively you machine. Certainly try to avoid any up-cutting on a powdercoated edge as this tends to lift the coating off.
One idea I had but did not put into practice was to pre-chamfer all the powdercoated edges with a tiny carbide spot drill. This separates the powder coated area that will be machined away from the part that remains.
An open mind is a virtue...so long as all the common sense has not leaked out.