If the machine is a router,the first cut will be skimming the spoilboard flat.The surface will be determined by whether the tracks are straight and in the same plane when viewed from the side.If your concern is about the amount that the beam of the gantry sags by as the weight of the Z axis moves,build some extra support.If you truly need accuracy,as opposed to resolution and repeatability then your project is probably outside the realms of what a homebuilt machine will ever be capable of.As an example;I have known an apparent increase of 0.006" of tool length as the machine went from workshop temperature to constant operating temperature.The high end machining centres will deal with this sort of thing.The price reflects the fact.