i've seen that hole for the roof rack on a few cars, usually it is plugged with a rubber bit and there is a recess to keep the bolt head clear of the door.
I found another one in my new Bravo. There is at the passenger site on the floor a tiny space behind a black plastic thing. It has the space of an ashtray. Really strange small place I really don't know why it's there.
My first thought that it was a hidding place for the Italian Maffia for placing some white powder or something. Who knows more?
Holes in the door frames are for the roof rack - fits no probs (although single-handed fitting both rails and bike rack has led to a few scuffs so I've got touch up paint to fix them!)