Could you please elaborate how that ends up as a Merkle tree?

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?

This might be complicated by the fact that "merkle trees" and git/blockchain invert the parent/child relationship. The root of the git/blockchain trees changes every time a commit/block is added, and the child nodes are called "parent commits" in git. Also the shape isn't going to have a wide base or be balanced like a binary search tree or similar.

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.