John -
These screw do serve some function in that they help prevent the top of the window channel from moving or flexing when winding the window up or down. Ultimately this may not mean much, but may reduce wear and tear on the little mounting studs at the very bottom the channel which are rather fragile. It should also help reduce body squeaking while driving.
Thankfully, these were precision drilled (probably with a jig of some kind) so the holes should line up no problem on the door skin.
The screws, if I recall offhand, are the kind with a panhead that has an integral washer-like surface integrated with the panhead. These will be posidrive, but save that Phillips here should be fine. On my BJ8, the original screws are quite long, maybe about an inch long.
I do believe they are #4 screws.