A bit complicated to explain, but since you have the cover off, you'll be able to see it in the flesh also.
The oilpump pumps to the outside of the oil filter, oil runs through the filter and then, in the RH side cove, is supplied upwards to the cilinderhead, and downwards to the crankshaft (with cover off, you'll see the crankshaft is hollow, that's how the oil gets to the bigend.
The bottom cover screw indeed looks special, but I wouldn't understand why it has to be. Where it screws in in the cover it indeed blocks a drainhole. Withe the bike on the sidestand, changing oil: by removing this bolt the oil around the filter will flow into the carter and out of the sumpplug. Then, with an almost empty filter housing, it is less messy to open the cover and take the filter out.
By installing a larger dia bolt you don't block any channels that I know off, but check anyway. A M6 helicoil with standard bolt works well too.