The bigger problem is when platforms block the content. In this case very few people will hear about the conspiracy theory. So then few will know that this is something worth investigating. This dramatically hinders research into the (potentially true) conspiracy theory.

I have less of a problem with marking things as unfounded if they are actually unfounded. I wouldn't use the term misleading because not all unfounded claims are false. There's still a lot of gray area here. Maybe the person in charge of making those judgements is not a subject matter expert. Or maybe the person making the claim has some additional information that cannot be revealed. (Perhaps they are inside the organization and cannot leak too much or they will be caught.)

I would set the bar for marking things as misleading as requiring evidence to the contrary. I think it is fine to mark things as lacking evidence, as long as that can be established fairly and reliably. I have my doubts that this can be done reliably, but as long as there is no blocking occurring, I think the harm of a mistake is minimized. Anyone claiming to be an impartial subject matter expert capable of making these judgements should provide evidence of that claim.