Sapper gives you the Foxhole state, which considers you to be in Partial Cover. Then the rule from Climbing Plus says that you cannot benefit from Partial Cover MOD. (doesn't say you don't have partial cover from scenery it just says you don't have the MOD) So it the end, you have Partial Cover from all direction but with no mod. But for the other effects of Sapper/Foxhole, i think you can combine them. We used to be unsure if we could deploy on a wall, now we know we can. So i don't see why we would not be able to deploy in foxhole state on a wall. And there is nothing in being on a vertical surface that triggers a Foxhole state cancellation clause.
i already hand waved realism as much as digging in a very thin metal sheet roof. Or digging in a glass roof.