[Andy]

It's because everything is broken into triangles. If you triangulate the final model, you'll see how it is ultimately rendered, where one surface can be broken into many triangles. Of course you could model in flat-shaded geometry, which would hide any of the slight plane/float-rounding variations. But that's probably not what you want.

The best thing to do is to minimize the larger surfaces areas before you do a boolean.

In this case, I used a couple of boxes as a knife-booleans to chop up the surfaces into rectangles, before doing the final cut-boolean. That reduces the surfaces area of the triangles.