Torsten did an update of the aerofly.exe. With this update of today the stripes of overlapping scenery textures should be gone.
Please report if any issues still exist. The current version of aerofly is EA4.68 (20170727).
There is still an issue with masking. At the border of custom sceneries I can see an area of low resolution, rather blurry. In a distance there is again the default texture visible.
This is under investigation and will be solved in a while.