Piece size is still baked into the file (as piece length), and is used for presence bitsets, which are a crucial part of the swarm algorithm. Clients download the rarest pieces first to boost efficiency, and this information is handled as bitsets shared between clients indicating "I have chunk {1, 2, 3, ... 50, 52, ... }".
Merkle tree roots will only be unique for each piece length. Piece length should still correlate with total size, to prevent huge bitsets-- a 16KB piece length on a 64GB torrent would have a 4 million item / 500KB bitset (!), so it could take 500KB of RAM per connected peer to maintain state-- or maybe compressed bitsets make this problem irrelevant in practice?
