In order to get rid of the whole completely, you would have to replace the inner and outer covers. the shifter spline rides in a tunnel that is made up half by the outer and half by the inner.
Once the shifter shaft is pulled out, you're left with the tunnel. It gets sealed by a circular gasket. The chrome cap really doesn't seal anything. So, if you were to replace the outer primary cover with one that doesn't have that tunnel shaft, you would have to somehow seal the hole (tunnel shaft) in the inner cover. This could probably be welded shut but who wants to take a chance on a leaker.
I bought an after-market plate that covers the little round cap. It looks pretty good. They are called primary inspection covers. Hell-of-a-lot cheaper than a new inner and outer primary cover.

 

Ok I see what is going on. (insert light bulb icon here)

There is a gasket that seals the inner primary tunnel the shifter shaft goes through, and the chrome plug just covers the hole and also seals the outer primary cover....and the two primary's go together, you can't mix them with forward control designed engines. (if you get my drift)

So this is my situation.

When I bought the bike, the deal included installing a primary cover with no hole in it.
By what I know now, (thanks to you guys here) in order for that to be done, they would not only have to supply me with a outer primary cover, but an inside one too.

If they agreed to do this as a condition of the sale of the bike, then they need to replace both, and if they didn't know that when they made the sale, then I guess they messed up.
Someone should have checked to see what was involved. If the whole engine needed to be removed, they should have accounted for that in the price of the sale.

Now I am under the impression that I will end up paying for the new inner primary, and any more labor so when it is completed correctly, the outer primary will not have a hole in it.

I am going down there on Tuesday, and have a discussion with the owner who made me the deal and get this straightened out.

Thanks guys, I will let you know what happens.

Wish me luck.

 

They could replace just the outer cover with one that has no hole and on the inner cover they could tap the shifter shaft hole with a pipe tap and put in a pipe plug with some sealer on it. That would stop any leak and would be quick and easy. You would have to use an inspection mirror to tell the difference.