Do I get away with the wrong screws and holes on a deck if the paint will cover both?
I think a bigger issue than paint sealing moisture out of the screws is whether or not the screws in question are made of a material compatible with your deck framing.

Pressure treated lumber (which your deck is hopefully constructed with) has a tendency to corrode just about anything you put in it, unless the fasteners are stainless steel, or have a ceramic/heavy galvanized coating. Lumber sold after January of '04 (in the USA at least) is especially corrosive, as lumber mills moved to a different preservative. 

If your deck was built with lumber sold in '04 or later, which I'm doubtful yours was, it's especially important that you use screws rated for use in pressure treated lumber.

I'd suggest looking at the box these screws came in, and seeing if they're approved for use in PT material.
If they aren't approved, I'm very doubtful paint is going to make any difference whatsoever.