Bitcoin transactions are not stored in a Merkle tree. That is just one way of representing them.
The most common serialization for blocks is just:
Header (prevhash, merkleroot, time, nonce, difficulty, version)
Number of transactions
Concatenation of all those transactions
This serialization is used on the P2P network in block messages, as well as on disk ...
Merkle trees in general are useful in the context of a prover-verifier model.
A prover Peggy wants to prove to verifier Victor that a merkle root R, which Victor knows ahead of time, commits to a tree which includes a specific leaf L.
To do so, Peggy would send the element L well as the Merkle proof (or branch) containing all hashing partners L is combined ...