I'm not with Laminar Research, just a fellow simmer in the UK, but could you please advise which airports this 'flattened area' is prevalent, I guess from your post that it could be all of them?
The only thing I can see from your log.txt file and the information associated with your scenery_packs.ini file that looks slightly out of place, is reference to the following files that appear to have been written for X-Plane 10?:-
24 Custom Scenery/zPhotoXP_+46+011_15_Bolzano_XP10_2018-05_overlay/
25 Custom Scenery/zPhotoXP_+46+011_15_Bolzano_XP10_2018-05_terrain/
Whether or not these files are causing your reported problem is unknown, but you might wish to consider moving them out of the Custom Scenery folder temporarily, just to see what happens?
Also, and whilst probably not relevant to your current problem, but I have noted that you have a number of aircraft as follows below, that were written for earlier X-Plane versions and which are now not compatible with X-Plane 11:-
Scanning of aircraft files is complete. Some of your aircraft files will not be available to fly in X-Plane, probably because they were created by a version of X-Plane that is too old. Aircraft that will be ignored:
0:00:15.818 W/ACF: Aircraft/C-17 Globemaster III 1.2/X-Plane 9 Aircraft File/C-17_Globemaster_III.acf
0:00:15.818 W/ACF: Aircraft/Extra Aircraft/Zenair CH 750 STOL/CH750.acf
Is it possible that you could have other files in your X-Plane 11 root directory that were written for earlier versions, if so, you may wish to consider a completely new and clean install?
Sorry, not much more I can offer at this stage :-(