Generalized Merkle Signatures, SHA-3 and Sakura
In general there is no reason to use tree hash modes for Merkle trees. The reason is that a Merkle tree itself is already some kind of tree hash mode. The important thing about this kind of mode is that it allows to compute the root node given the value of one leaf and one node per tree level. 

The possible ambiguity of hashes is not relevant for hash-based signatures as for these the tree height and thereby the number of leaves are predefined.