[304065]

That looks like some prior owner snapped the bolt that goes there. Studs on the lower two holes, bolts in the uppers. Probably decided to really torque down on it and then crack. Couldn't get the bolt out so just ground off the jagged stub and left it.

No, those holes don't go all the way through. They thread into bosses cast in the aluminum of the case. I would thoroughly clean everything, cover the gap between the flywheel and case with something so you don't get chips in there, use a good punch to mark the end, then carefully drill the stud, starting with a small drill and working your way up, and use your e-z out with plenty of heat from a heat gun and PB blaster to ease the stub out.

The reason for the elongation of the hole is that somebody tried this and gave up. Probably because the drill couldn't get a purchase on the end of the stud. Hence, a good punch and the graduated drill trick are key.

It doesn't sound like you plan on splitting the case but with it torn down to the crank you could probably take it to a specialist for extraction, but I would be infinitely cautious of chips falling into the open case. If you were closer I'd say "send it to Ollie's" but alas Lake Havasu, AZ is a long way from Hertfordshire!