Ever since the release of the editor, i haven't been actually playing the game much, just map editing. :D
While building my map, i've noticed 2 things, well actually i noticed one, and my friend noticed the other. If you dip the terrain to the lowest point possible (i recommend trying this on the space template), you can land units there, BUT your camera will not dip all the way down to that level. Another issue is when you try to land a cc on it, it actually raises the terrain, by a lot actually. I'm not sure the values of depth, but i'm sure my terrain was in the negatives and the rise brought it up to 0 or somewhere around that level.
Likewise, if you build the terrain at its highest there are issues. You can't really bring the camera that high. Another problem is that if you try and land a building there, it actually pushes the terrain down to "make room" for the cc in what i assume is an invisible ceiling. If you lower the terrain by a just a few nudges, it'll be fine both for camera angle and building.
just discovered something else about this bug. Every time you place a building in a severely angled area (lets say you want to place a bunker on the side of a steep hill), it will modify the terrain. It will flatten it.
I found out while making a concave island. I wanted the interior to be deep and have the minerals be on the raised edges, and when i went to place the cc there (in the game), it flattened the necessary area to place the cc. Likewise happened with the barracks, factory, nuclear silos and starport.
I think it more has to do with engine limitations than "bugs", for example there's a lot of clipping when you build on angled terrain. Remember, this is a game engine, not a video game, limiting controls and freedom isn't a concern for editor. You can just lower/raise the terrain if there's issues appearing (Water only goes for like -24 to 24 height wise, so I don't think extreme use height was intended for the campaign and game, but felt the should leave the option for map editors). If you haven't noticed, all maps so far are completely flat and have no variation in high besides for cliffs, this may change in the campaign, but I also expect it will have no build zones in there's areas to prevent clipping.
If you look at the building in the data editor (I don't have it in front of me right now - but I think the actor for the building) at it's events you will see that it has things like "OnConstructionStart: FlattenTerrain" (not verbatim, but that's the gist). I wasn't sure what this was doing, but now I suspect it's what you're experiencing.
You might get "undocumented" behavior if you remove the flatten terrain events - If you'll notice raising and lowing the terrain without specifically using cliffs never blocks line of sight either. I suspect that terrain height changes is meant specifically for aesthetics at ground-level, but not to change gameplay in any way whatsoever.
What you need to do is remove the "OnConstructionStart: FlattenTerrain" actor behavior from the building and allow it to "roll" with the terrain as well. This was a property in WC3 if I recall, but I haven't looked into the data editor much.