Project Update:
I have examined the Rivers shapefile, and did find some strange features, like the one in the picture below (using QGIS), and some shapes with a negative zed-order (corresponding to tunneled parts of the Rivers), but even after eliminating this odd features, the problem persisted. It even persisted after getting the rivers from the overpass-turbo query "Waterway = River" and then exporting the Geojson to shapefile.
The plan for now is to generate the scenery with no rivers, but all the other features. A test scenery I have produced, still with no rivers neither roads, shows a more varied landscape with diverse land classes and improved elevation mesh. The airports are now 3D, with slope runways with an "arching" structure which globally gives better results than the previous flats. The groundnets, as expected, are now aligned with the scenery, namely the markings.
I have also added the osm2city buildings from merspieler, and the overall result looks great.
Off course, there are still much room for improvements. For instances, the land classes are prepared for a summer in the southern European region, so this results in rather arid landscapes in the Azores, which are not realistic. The regular landscape there is predominantly green all year round. It is not a "Mediterranean" kind of landscape, but pretty much "Atlantic"!
I plan to have a working scenery you might download during this following week (28 june to 4 july).
The "strange" rivers I found in São Miguel island: