The game by default, classifies thick stone roof as overhead mountain, not sure if that if possible without creating a separate roof type.

I understand, I placed a skylight window from dubs skylights mod on the roof and so far its ok.

That might be ok due to how the game handles overhead mountain terrain. If the space encompasing overhead mountain you constructed is now lowers that the minimal required (due to building skylights) then it will not spawn infestations. @Lanthrudar, it is possible, take a look at Raise the Roof 1.1 and you will see that his stell thick roof is coded to not spawn infestations.