shouldn't "på vilken nivå är du?" be an acceptable answer here?
Perhaps, but where it's reasonable and idiomatic, we like to keep the sentence structures the same.
Can this refer to both physical levels of, for example, buildings and levels, for example, in games?
It is a fact, though, that "på vilken nivå är du" is (at least) as correct as "vilken nivå är du på". Can't you simply make the program accept both?