If one corder is too low, just adjust the bed leveling screws until it is level.. it shouldn't matter if the glass sits lower on one corner, that's why the bed leveling screws are there...
Ditch the stock calibrating method, and do a manual leveling.. this will solve the issue..
And the reason why there is not 4 leveling screws, is because the 3 screw method is much easier to use, but there is a technique to it.
When you adjust the back left corner, it also effects the front right corner, and vise versa.
If the front-right corner is too low, lower the rear-left corner, and the front-right corner will raise.
Remember, adjusting one corner, affects the opposite corner as well.