they would have known true clearance all the time, because all commercial aircraft do have radio altimeters, and they are pretty accurate, even though the display would have been smoothed out, that data is going to show exact measurements, though likely not too well, as the roof is synthetic that is more or less transparent. But definitely they did practise during the week, and they were confident that the weather was cooperative, as otherwise that fly over would have been at 500m if there was any sort of turbulence across the stadium, as this is a well thought out contingency for weather. clear still air, you can go down to planned altitude, and even if an engine flamed out from a bird strike, they had both going near full power before the fly over, so no lift compromise really, and even if they did get a bird, it would likely have just been served on the field as bird a la king, with a side of shredded feathers.
Louis Botha does have a history or rather regular bird strikes on take off and landing, and both Toyota and Mondi are still there, the most likely impact points along that runway. they finally figured out the way to keep the seagulls and geese away, as the guns and hawks did not work, was to not mow the swamp, which was a great relief to my friend, as he was one of the drivers of the 2 heavy wreckers who had to go out, with another as ATC relay, and go recover the tractor wherever it had bogged down. So now they do not mow, and it is back to being a wetland, and Toyota's parking lot.