You're right that Spectre and Meltdown are not related to SMT, but that doesn't invalidate the wider point about hyper-threading and side-channel issues I think.
Parent may have simply meant TLBleed/L1TF (Foreshadow) instead of Meltdown/Spectre.
I'm not trying to invalidate any wider point about hyperthreading, and the original article wasn't trying to make one.
It was specifically about Spectre and Meltdown mitigations which are unrelated to hyperthreading, so testing with or without hyperthreading is fine. Bringing up hyperthreading here is like bringing up how a diet high in salt is unhealthy, someone pointing out that salt has nothing to do with the original article, and then a final comment "Yeah, but that doesn't invalidate the wider point that we should consume less salt!".
Parent may have simply meant TLBleed/L1TF (Foreshadow) instead of Meltdown/Spectre.