As I recall that hole may be a mounting point for a temperature sensor. Which is pretty much useless, anyway. By the time you get a reading on a temperature gage that a catastrophic failure has occurred, the motor is already toast!
Water pressure gage is a much more reliable indicator of the health of the cooling system.
Back to your gasket, as the O.P. said, sometimes gaskets and other "consumable" parts are sold in multiple increments, to save money on packaging/stocking. Sometimes there are more gaskets in a kit than you need, 'cause it's cheaper to throw all the gaskets needed to cover multiple models than it is to have a separate set for each model.
Many of the older Inlines didn't have the temp gage hole, instead the hole at the #1 cylinder spark plug "pad" was round instead of oblongated.
If you were to use the round-hole-gasket on the above motor, it'd probably leak if the gasket didn't cover the entire area (and vice-versa).
At any rate, only one gasket is required, use the one that fits the cover configuration.
If you find the spark plug pads are eaten-away from corrosion, clean 'em up and use a bit of non-copper RTV. Hi-Temp Red works just fine. As does Ultra Black or Ultra Grey, for example. But the Ultra Copper isn't recommended, due to the potential to set up an aluminum-copper-aluminum sandwich corrosion cell.
Hope that helps, G'luck with the repair.........ed