Your right on track Chef Wong. Dry fitting the stone and using the pencil is the simplest way to do it and will make for a perfect fit. There is no need to remove a ton of material but enough that there is no need for a grout joint right under the slab sill.
The back cut on the back side of the slab will make it fit tight to the window (or a hair off for silicone). This back cut will also create a half dado joint for the silicone to bite better.
My favourite products up against plastic windows are Kerdi Fix and Hydro Ban. Hydro Ban seems to bite better to plastics in my limited testing into this.
But nothing bites better than Kerdi Fix at this connection point.
You could use Noble Seal TS and Noble Sealant 150 if it is a steam shower but because the plastic windows flex I like the rigidity you get from Kerdi Fix. Kerdi Fix sets up a little harder.
Hope that helps.