That wasn't the answer I was looking for, but thank you for answering anyway.
That was the only answer you could get, since there are two issues at play here, and both contributes to the problem:
1) Meshes doesn't always have the correct altitude. All meshes have some kind of vertical error, depending on source data. In order to overcome this, Microsoft default mesh has been pre-processed to "smooth" the elevation differences between the airport and the surrounding mesh, for a number of miles around each airport.
I don't know if other mesh developers use this method but, if they don't, it's almost sure to have the "plateau" effect around the airport. Of course, provided the airport HAS the correct altitude, which in case of Geneva is 1411 ft, like in our scenery.
Which bring us to the 2nd issue:
2) FSX/9 airport can't be sloped, an airport is supposed to have the same altitude all over its area, otherwise there would be huge problems with floating AI, flickering terrain, etc. Geneva, in real life has a mildly sloped runway, which is also located slightly below the main apron because the two ends are at 1407 and 1365 ft, the main apron, which is also the "official" published altitude, is at 1411 ft.
We might have chosen some kind of halfway value between 1365 and 1411, but it would have been wrong at all places, and might complicate things like AFCAD, AI, alternate AFCADs made by users, etc.
So, we don't really have any other choice that placing the scenery at 1411 ft but of course, if an underlying mesh is representing the sloped terrain AND it also adds its own error factor, such problem are likely to happen. You don't noticed that with the default mesh, because of the above pre-processing.
I will endeavour to make my own blended flatten at some point and make it available as freeware to all Switzerland Pro X customers at some point in the future.
This is good, and it (IMHO) should have been done by Swiss Pro developers, because the thing that has to be fixed is the mesh, the airports can't really be put at any other altitude than the official published one. They might have used a similar technique Microsoft used to smooth out elevation differences between airports and mesh, which is probably what you will need to do to fix the problem.
If and when FS engine will finally support sloped terrain for runways/aprons, these problem will be hopefully gone.