The .torrent file only stores the merkle tree's root hash for each file, and the torrent client will query it's peers to get the rest of the merkle tree (verifiable against the root hash). The leafs of the merkle tree are the hash of each 16kb block.
Interesting consequences of this:
Piece size isn't baked into the file anymore (and I've seen torrents with 16mb blocks), the client can dynamically chose it's verification piece size by requesting only so many layers of the merkle tree. Or it could skip requesting the tree and verify the whole file at once.
Merkle tree roots will be globally unique. You can scan torrent files for duplicated files and download common files from multiple swarms.