How to ensure the wax seal on my toilet is set properly?

From my experience, the wax rings of today are a little softer than the ones years ago and settle easier. Using an oversized ring is bad because it can squish out and impede drainage when flushing. You were smart to raise the flange a hairline above the finished floor as that will also ensure a proper fit. Using the one that came with the toilet was also smart because the rest of your directions would be based on the ring they included. You probably caulked around the toilet after setting it in place. I have always left a weep hole in the back just in case a ring started to fail, you'd see signs of leakage.

Toilet water level decreases a bit after a flush but stays at that level (assuming toilet flange).

There is no relationship between those two factors. The level of the water in the bowl is not dependent on the wax seal. The seal only prevents leaking during the flushing process as water is passing through the trap and past the wax seal. ( All toilets have built in trap between the bowl and the flange ) After the water has evacuated the bowl it passes from the toilet to the drain pipe in the floor, That connection is sealed with the wax ring.

It was pretty hot that day and the wax was extremely malleable.

If it was extremely malleable then you would not feel much resistance but that does necessarily mean that a good seal was not achieved.

I flushed a few times, no leaks appearing anywhere.

A leak, if there is one, may not be visibly detectable . If there is path for the water to go down through the floor you may not see any water appearing from under the toilet on the floor.