Hmm i messed around with a few different settings in PlayOnLinux trying to fix this problem and it seams being more related to Settlers6 version rather than Wine versions.

According to (bugs.winehq.org/show_bug.cgi?id=39080) version 1.7 of Settlers 6 introduced the problems with glitcy terrain and i've reproduced the error on Wine 1.6.2, 1.7.42, 3.2

However i was able to get the game running without the terrain glitz following the guides from winehq (appdb.winehq.org/objectManager.php?sClass=version&iId=17245&iTestingId=97315)

This is my setup:
Running wine 3.2 (32bit) in PlayOnLinux container on Ubuntu 16.04 (Wine 1.7.42 seams fine as well)
Enabling "directx9" under PlayOnLinux->Configure->Install Components
Setting: "VideoMemorySize=256" & "OffscreenRenderingMode=fbo" under PlayOnLinux->Configure->Display
Download and applying NO-DVD fix, for version 1.5.4 (Find the right folder: /GOG Games/The Settlers 6/base/bin)

This solved the problem I have however not played far enough in the campaign to see how the nocd patch for a lower version handles the extra material included in the GOG gold edition.

I found the NoCd patch on a gamingsite I found "trustworthy", in my mind all sites offering to host NoCD patches and the like are notoriously sketchy, but I was running out of options.

How this helps others in the same situation

Regards