The thing is, customers don't necessarily want a distributed messaging system, they might be perfectly fine with a decentralized one if it supports E2EE. Matrix went the way they did and it's far from obvious whether it was a good choice. I'm leaning towards no.
> but someone's done it three times
You can do it however times you want and it will be easy to do if you have access to one of the few domain experts of the protocol. It can be considered easy to implement once someone else successfully implements it and continues to support it for a significant period of time. Rewriting one thing three times inside a single org is not something of interest.
> Blockchains are Merkle trees
This is getting offtopic, but anyway. Blockchains are DAGs, they are not necessarily trees. The canonical chain and candidate blocks have only one genesis block, and non-genesis blocks could have multiple parents (e.g. one main parent and orphaned uncles), which by traverse still converge to the same genesis block.
Although Merkle trees are used in the underlying block data structure, this is orthogonal to the blockchain concept and any data structure could be stored there.
> MLS
Unless I'm missing something about MLS, you're mixing unrelated stuff here.