Sentence 1 sounds more natural to me too. But you have changed the idea of the sentence. In sentence 1, we are told about the room. The room is important. In sentence 2, we are told about the junk. The junk is important. The facts about the room and the junk are the same but the focus is different. I also agree with Scott's rewording of sentence 2.

Both are natural. For #2, I would say "piled up" rather than "piled". To see why, consider these two possible answers to the question "How high is the junk piled?" 1) The ceiling 2) Up to the ceiling Clearly #2 is a better answer because #1 doesn't answer the question "How high?". For the same reason, you want to say "piled up to the ceiling" in order to specify how high the junk is piled.

Hi Bean, They all sound as natural as each other. However, in #1 you emphasized the room. If someone asks me about the room, that's how I would answer. In #2 you emphasized the junk. That would be how I answer if someone asks me about the junk. Hope that it helps! Teacher Daniel

Yes. To me, sentence #1 is more like native speaking than #2. I think this is more concise. The junk in the room is piled to the ceiling.