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My phone's dead so I can't take a photo, but when I aligned them and compared the levels, the low level line on the bigger window corresponds pretty much exactly to the middle between top and low level marks on the small window cover.

That's interesting, so was the big-glass high level line above it's counterpart also?

I'm wondering if this means as well as the larger sump they also decided to run a higher oil level.

I'm not sure how many different clutch covers there are, but if you Stan, have a 4.6 and a 5.3 - I have a 6.2 litres. There is no difference in size/ dimensions of the covers.
The variables in the oil volumes is dependant on the oil pan/ sump size. Oil volume has nothing to do with the clutch cover size.
Over the years , engine parts have been swapped and sold - so some owners wanted the big oil pan for greater volume but didn't want to change the clutch cover / bigger sight glass to match the oil increase. And conversley- some wanted just the bigger sight glass to better identify where the oil level was at. So once again the miss match between clutch cover and oil pan.
So in other words, when the bike was new , if it had the big oil pan, it also had the big sight glass on the clutch cover - the 6.2 litres stamped on the cover actually matching engine oil quantity. Most , if not all 1979 models had the small pan and small sight glass clutch cover

If I draw a line from the top oil level line on the 5.3, it hits exactly the top of the glass of the 4.6.

I am not sure, I'd have to check it. But if there is 6.2 stamped on your tackelhappy, I think the one on my bike might be a 6.2 liters as well. If so, the cover itself will be the same shape and size as the other. Same window as the 5.3.

Checked one of my manuals. There does appear to be 3 different oil volumes for engines[/attachment] listed.

If there is only two different oil pan volumes , and all clutch covers are the same size, then how is there 3 oil volumes.

No idea, but the 79 oil pan is way different than 82. 82 holds more oil, I think it's deeper, that oil pick up is also longer.
There might be no changes in overall engine design, but a deeper oil pan with different passages might accommodate some of the extra oil. Also, and again I am just blindly speculating so feel free to hang my by my balls while I'm not guilty of assumptions, hahahaha, maybe the oil filter compartment hold a bit extra oil as well?

This relates to my other thread I just started about cross reference. Basically, I'd like to put an engine together from scratch, from different all over the place parts. I'm trying what fits where, and what are the universal interchangeable parts, as well if it is possible at all using a generic 79 - 82 or whatever crank case.