Hi,
I made this road like model. Then selected the faces to make a landscape on the left side with ‘Extrude Along Normals’:
This is what happens:
Is there something different in Blender which auto merges the intersecting vertices / faces etc.?
Thanks in advance. 
Not that I’m aware of (hoping someone can correct me).
This is a very difficult vector problem (very computationally expensive and hard to implement a general solution) - CAD software like Solidworks have mathematical methods that solve this and then still only in special cases… doing it with vertices is something that even paid-for software like Maya don’t do automatically… so it’s not unreasonable that Blender can’t do it.
Best you can do is manual cleanup after the point in your screenshot:
That will only get rid of the intersecting faces, so you’ll still need to select the remaining overlapping vertices and dissolve or merge them.
Sucks that there is nothing to automatically do this (yet).
Good luck.
Or… when it starts to overlap you have to stop and maybe don’t use the verices in the inner curve… or just fill up a bit more manullay… like so…:
Or maybe have a look here:
