I really don't see that as a problem. Having transperancy of the money supply is one of the most important things that make Bitcoin special. Think about it - you can never really know how much gold or dollars there actually are in the world. You can have an estimate, but not an exact value like in bitcoin. CoinJoin solves the issue of fungibility. You can't claim for sure who owns the coin joined bitcoin. And if enough people used wallets that have coinjoin then bitcoin becomes even more fungible. This is a good way of doing it as it's an "optional" feature keeping the base layer as pure, generic and effective as possible allowing things to be built on top of it. And, perhaps one might argue the lightning already improves the fungibility of bitcoin by a large factor.
I think fungibility and transparency of money supply are two separate things. No reason you can't have both.
That said, thank you for making the point about fungibility being better off as a wallet-level concern by way of widespread CoinJoin implementation.
I hadn't considered this before (that is, the optimality of making it an "optional" feature keeping the base layer as pure, generic and effective as possible allowing things to be built on top of it.).
Not sold completely -- but you broke my previous conviction and have me thinking about it now 😄.
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