There are unfortunately not enough people that hold this opinion, too many are trigger happy on defederating from those they don't like.

Like you say, there can be some legitimate reasons, such as bot servers, and I would add if a big company created an instance to take it over and kill the federation.

But too many simply do it because they disagree with what the people in an instance are saying, and that hurts the federated nature of the fediverse.