That has not been my experience, Mike!
Have found plenty of 109 wreck recovered legs with the aircraft Werke Nummer stamped into the top – just as per the image in the original post.
The Flying Heritage creation was a reconstruction that utilised original parts sourced from other 109s as well as newly fabricated parts, of course.
To a limited extent, I was familiar with its build in the UK (as was at least one other on this forum) and helped source one or two parts and it would probably be possible to identify the aircraft they originated from. Each will have the four-digit number stamped into the leg. If the legs on the Flying Heritage 109 are ‘original’ to the airframe (which I doubt) then different numbers simply mean that replacement legs, probably from other damaged airframes, have been fitted. We have found wrecks where one leg number matches the airframe number, and the other does not.
A case in point is the discovery of the wreck of W.Nr 5095 and where both legs were stamped with that number.