I'm not sure I follow that logic. The anonymity from using ChipMixer does not rely on an attacker not being able to tell an output came from ChipMixer. Indeed, it is trivial to identity a ChipMixer output, given their characteristic funding transactions with 50 outputs of 0.016 BTC, or similar. It is therefore irrelevant if an output is legacy or Bech32 - it can easily be identified as a ChipMixer output either way. Rather, the anonymity comes from being unable to link these outputs to any inputs due to the time travel funding structure and set chip size.

I for one would personally like ChipMixer to upgrade to native Segwit outputs at least, even if they keep legacy deposit addresses to maintain compatible with other services.