On automatic that hole is used to undo the torque converter bolts. I have no idea why is it there on manual, except maybe it is same part on both. Perhaps maybe it is to insect if crank seal is leaking?
Before I fitted the double hump cover, I ran for about 5 years without the bottom half D cover on the old backing plate and never had any issues. I wouldn't wory about it too much. You could always make one up out of sheetmetal and pop rivet it in place.