Look down upon can mean "considering someone or something lesser or inferior in some way", but can it also mean look down from a more elevated position? If not is there a phrasal verb for it?
Yes, it can be used in either way. You could even say something like
The bullies looked down upon me as I crawled in the dirt. "Fair enough," I thought, "I look down upon them."
In fact, the definition "considering someone inferior" is a figurative reference to the more straightforward physical situation.