Ladies and Gentlemen... Welcome to the 45th Annual Gotcha! Awards...
<big band fanfare>
There are three gotchas to be awarded tonight...
I was pondering things as I rebuilt to my SSD yesterday; and got to thinking more about EHAM and mesh. Until this point, I'd been thinking of Amsterdam as a collection of 3D objects sat on top of whatever mesh was underneath. It [somehow!] hadn't occurred to me that the 'excavations' for tunnels etc. Emilios referred to weren't so much just objects beneath the elevation of the airport surface & buildings above, but perhaps a local terrain mesh, whereby as in 'real life' the excavations were a physical reduction in height of the terrain rather than simply trick object placement.
I wondered then, if the weirdness I was seeing might be a function of mesh resolution.
Our first award, for 'taking his bleeding time to figure it out', goes to FactionOne! ...In my defence, the next thought I had was to check the manual for any note about minimum recommended mesh res., but as I was still putting back AS2016 and the rest, I didn't have Amsterdam installed to check the PDF.
Today I began reinstalling airports, starting with Amsterdam.
Side note: I had setup weirdness again, but slightly different - no Prepar3D.exe error (I think it helps to have started and shutdown P3D at least once since booting before calling it with arguments to add scenery library entries - but this is an unproven hunch at this point), but the Libraries weren't added to scenery.cfg (LC & AMS OK) - a few seconds in Notepad++ later, I started P3D. I found (as with my first install(s)) that I've no Type 1 Safedock anywhere (I guess that'll be fixed by the modified files in the zip previously posted).
I made my way to QA-corner and as expected, found it a little confused. Then I went into P3D settings, and increased my mesh resolution from 19m (I ran 1:1 with FS Global res. to prevent unnecessary tessellation) to 1m (figuring that tunnels are built to tolerances a little finer than 19m!)...

- 2017-1-22_12-54-14-685.png (3.7 MiB) Viewed 2178 times
Now certain that I was on for my second 'gotcha' - I went to have a look at the PDF, and sure enough it advises 2m or better resolution to prevent artefacts around tunnels
Our second award, for 'taking so bleeding long before R'ing T F'ing M' goes to: FactionOne! We present our third gotcha! to Emilios, for his supporting role in 'not telling Rob to RTFM'
More than happy to take it on the chin that I've been a dope all along, and get back to enjoying this wonderful scenery(!)
Rob.
NB: Emilios (and Martin) - sincere thanks for your time, help, and patience [and again, this epic scenery]. Hopefully this has been at least slightly useful for coming-up with stock reply no. 1: "Hello, technical support; have you set your mesh resolution?"
Right, I'm going to put the revised VDGS files in, and do some flying!
[Please feel free to edit/merge posts as you see fit to save other 'dopes' having to trawl a long thread before finding the magic bullet

]
EDIT: No Type 1 Safedocks with vdgs.zip modifications or anything else I can come up with - restoring my last differential image to install Vienna first (it does seem to like that!).
EDIT EDIT: Still some oddness with Vienna first (I had to add Libraries to scenery.cfg manually), but Safedock Type 1 working now (not sure whether because of Vienna first, or [re-]selecting the already selecting Type 1 for AMS in the configurator.