ROB
I have never been involved in the testing of prototype aircraft nor in the writing of flight manuals, so I cannot say with any certainty how it is done. But almost everything in aerodynamics is a matter of making a prediction then proving (or disproving) it by test flying.
In the manuals that I have examined these speeds have been stated as single valuse, or in tables to allow for things like varying altitude and temperature.
Best angle of climb at the stall is unlikely to be the best achievable overall. You are correct in saying that both thrust and drag are increasing as we decelerate close to the stall. But if you look at a typical pair of curves, the thrust curve is comparatively shallow in that area, while the drag is curve is very steep.