Hi Steve -
Firstly. let me apologise for the problem you are having - we should have done better on the first try. I will discuss with our Service folks, and get this put right. I will also have the plane you received run through our CMM (coordinate measuring machine) to report back on what the actual tolerances were.
A few general comments on measurement -
1) seeing light under a rule or square is a good way to identify a gap - but it is not a good way to measure magnitude. Light has a tendency to reflect at low angles of incidence, and gaps will look twice the size they actually are (which is why it's a good indicator test!). Best practice would be to then measure any gap with a feeler gauge.
2) Where "flatness" is is more important than overall flatness. For centuries, planes have been made with hollow portions of the sole, corrugations, circular voids etc. . Generally - hollows are no problem - it's convexities which really affect performance. Our tolerances are based on a plus zero, -.00x" - so from perfectly flat, to a little bit hollow, but within a tolerance. Your plane sole is defined by a locus of points that traverse the wood... not just a single area or region. Putting these points in motion makes a the plane blade follow a dead straight path. That why wood bodied planes can work as well as metal bodied planes - despite any sole variation due to wood movement.
3) Smaller planes may have proportionally larger visual differences in flatness - a .001" gap in a 1.5" sole will look much larger than a .001" gap across a 3" sole. From a production standpoint - smaller castings can be more difficult to machine, as there is less cross-sectional area to distribute clamping forces in fixtures - castings will "bow" when clamped, and flex back when released. Given the shape of plane bodies, some degree of hollow is virtually assured. Perfect flatness will be very difficult to achieve with surface grinding alone - a lapping/linishing process would be necessary as a final step.
Nonetheless - there is clearly an opportunity for us to have worked through the issue you have differently, and we will learn from this.