No…I am not asserting that. There will be some compression of the glass, as well as of the table.
On the table, the glass will experience linear-ish compression of its upper mass pushing down on its lower mass. Now pick the glass up and hold it in your hand (the normal way of holding a glass): it will be compressing downward above where your hand is, under tension below your hand and under circumferential compression where your hand is maintaining a grip on it.
You are confusing gross and net forces. Forces are vectors, which means they have not only magnitide (size), but also direction.
To figure out the net force, you can vector-sum the component forces.
The falling apple has one force, gravity (neglecting air blah blah blah). The resting apple has two forces acting on it: gravity and the upward force from the ground.
The gravity didn’t change, just that another force has been added.
You can compare net forces and see the difference is weight vs 0. You only see the paradox because you are only looking at one vector for both cases.