I looked at those holes for the screws, and they won't thread in with where the factory set it (hope this makes sense).. so I am afraid to use this method.

They sell a centering cone also, is that going to work better? Do I need a template guide to use the centering cone? I think it's BS that you have to pay extra to center your router?

The only time you need to have the router bit perfectly centered in the base plate is when using a guide bushing to trace a jig, like cutting dovetails. I center it visually during setup. Put the guide bushing on the base plate and the base plate loosely on the router base. Insert the router bit through the guide bushing and into the router collet and tighten. With the bit tight in the router, you can visually center the base plate by looking at the tiny gap between the bushing and bit.

The centering is required when changing base plates, since the manufacturer cannot guarantee the different base plate makers---you can even make your own baseplates----will get the plates centered.