In a merkle tree the leaves are not linked and they have a tree structure of parent hashes on top. Git and Blockchain nodes are linked and the fundamental architecture doesn't need a tree structure of hashes on top. While this tree structure on top might be useful, it would be an optimization, but not part of the fundamental architecture. Again, what am I missing?
When you say that "git and blockchain nodes are linked", I think you might be not abstracting the concepts from the form the data usually takes. For instance in git you might be thinking of a commit as a single package with all its source changes, headers, parent details and hash, but it terms of it being a merkle tree the leaf node would be non-hash parts (source code, non-hash headers etc) and the "tree on top" would be the hashes. This tree structure of hashes are absolutely part of the fundamental architecture of git/blockchain.
Using the hash of a parent node as input to a nodes hash alongside the nodes data creates a link, but it doesn't create a merkle tree. In a Merkle tree the parent node is the hash of the hashes of its child nodes and only leafes have data. These are entirely different definitions and also serve completely different purposes (linking to a parent node vs efficient lookup of membership of some data in a larger dataset).
Could someone clear up my confusion and explain to me where Git/Blockchain use a Merkle tree in their fundamental functionality? Or is the term Merkle tree simply misreferenced a lot?