There's no 'autogen' as such. The positions of trees and buildings not controlled by facilities is governed by the .lso files. These start life as a black bmp version of the scenery sheets which have a white dot placed wherever you want a tree or building to appear. What the dot represents is defined in the scenery mos file and sceneryobjects.xml. They are not editable without special tools for which M$ negated to provide a working set! I do have a semi working tool which Johnno passed onto me years ago but it's a bit long winded and hit and miss to use.
To remove the autogen you would need to either remove all of the .lso files or modify the sceneryobjects file. Incidently in this file you can change the tree types or building types etc. to add a bit more variety to your landscape. I swapped a lot of coniferous trees to deciduous, for example.
I've checked all of my installs which have or haven't got the shaders in and none show what you are seeing James! I'm guessing you've fiddled about a bit too much!