This just says that the 109 performance was quite certainly above the 500 kph minus 5% and would in no way exceed 500 kph plus 5%. But where should be the S/L speed be set for the 109 ingame?

The specification says NOTHING about average performance. The 500 kph is a fully theoretical value and was never meant to reflect real average performance.

I also highly doubt that the average 109 reached 500 kph and all tests indicate that it did not reach this value.

My guess is that the average speed at s/l was somewhere between 475 and 485 kph considering the flight tests.

If the average flight speed was 500 kph one should find flight tests showing individual 109s with speeds ABOVE 500 kph. I have never seen anything like that.