Stubborn stains indeed!
What you are seeing is the factory glue coming through the headliner.
As I see it you have some choices:
Remove the glass and replace the headliner
or
Mask off the edges of the headliner & spray with a fabric spray paint (Duplicolor or Rustoleum make products). The paint really stinks, wait 'till warmer weather to work outdoors.
or
live with it.
