No windscreen/gass cover doesn’t cover a glass roof. Its also not to be taken for granted insurance would cover it in all incidencies. Although I would expect RSA or Direct Line when they take over next year on scheme cars. Something to ask your insurer if anyone got a private car with glass roof, as it seems some do some don’t.
If it was just a crack I can see them giving you the option to live with it (as they do with accident damage), but if it’s letting in water then they’d obviously have to authorise a repair. The customer would then have to pay the accident excess.