Hi,
Fileting the top after flow is a problem of the flow.
The sides of your object are flowed too.
If you hide the top side, you will see it.
You could delete those two faces, then separate and rejoin all the faces then you could filet the top border.
If you prefer, you could blend intern and extern top edges, or sweep an arc to avoid edges created by filet.
But, you could filet before flowing.
For the bottom side, I have done an extrude of the edge.
Then I resize the x and y to permit a boolean union.
Before boolean union, I move up this cylinder for fileting the bottom.
At the end, I filet inside the glass.

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