It's probably a good idea to make buildings climbable, or add steps or ladders or something. I personally dislike having terrain accessible by flying model only.
Not sure about walking part way up. Without looking at the rules, I'd probably allow it. Don't have the book with me now though...
Yeah, I'm pretty sure it's always base to base. Since model's height is not accurately represented by the model, and the Ht trait is used instead. Base to base is the only comparison that makes sense.
If you make a small wall impassable and climbable, I'd subject it to the same rules as climbing in general. It's a little bit tricky as a model can't really stand atop a fence, so I'm not sure. In this case I'd probably make the model stop, and clear the entire wall in one action.
We usually treat trees in a forrest as part of the forrest, just like you describe. Separate trees outside of a forrest would be blocking and hard cover.
If it's a graveyard, I'd probably say that the whole yard is severe.
I hope that helps a little =)