Some comments:
If you start with 1.5" plate and machine it down to 1" by taking material off only one side you may encounter serious warpage. You mention stiffeners, presumably welded, on the backside but your description suggests there will be largish areas between the stiffeners. It is possible you could find the top surface after machining tends to go convex in the areas between the stiffeners by more than your hoped for 0.005".
But perhaps you plan on normalizing or stress relieving the whole thing after fabrication in which case no problem.
Regarding the threaded holes/counterbores I would suggest you get the counterbores bored separately from the tapping hole. It does not matter if your tapping hole wanders a few thou but you do want you counterbore to be accurately positioned.
An open mind is a virtue...so long as all the common sense has not leaked out.