I was thinking about drilling the holes on the inside because I assumed that the window is sealed to the outside. Since the water I will be shedding will be from the inside, I thought it might need extra holes. I will check it out though before drilling.
I am a little fortunate that the window is set close to the inside wall surface, so there shouldn't be much of a ledge or shelf at the window sill other than the window frame. I was also using tile in my language because it mad eht discussion easier. I will probably end up using a solid surface material for the shower walls. Then all I have to worry about is the caulk.