I understand the czech sentence as "Which building are you going into, which building are you entering?". Isn't the suggested translation "To which building are you going?" something else, like "coming closer to a building" - "ke které budově jdete?" ?
I think you are right that the Czech sentence means that you enter the building.
To me, the English sentence implies that you're going to enter the building even though it could mean just go to the location of the building.
I can't think of any alternative English sentence that means "I'm going to the building and also entering it". Maybe this is one of those cases where the languages don't line up with each other 100%.
Just to clarify: no alternative English sentence that anyone would actually say :)