f people are worried that Threads will affect likes and comments (and therefore like/comment-based sorting algorithms) on other instances, it should always be possible to exclude Threads’s contribution to those metrics, no?
That's one of the effects of defederating. And you are still ignoring the overall point of the comment 2 layers up from your reply.
Really I think you are losing the forest for the trees. Meta/Facebook/Zuck is a known quantity. They will corrupt and exploit any environment they are a part of via any means they can. We don't need to be able to predict every last detail of how they will do so to know it is true. They have a track record of being awful, anti-consumer corporate citizens. WHY would we want to try to invite them in and try to contain them? Can we make the fediverse invisible to them? Of course we can't, but why would we cooperate in any way?
Folks who don't think this is a problem can use an instance that federates with them, just as I've chosen ( and will always choose) an instance that does not.
There is no reasonable argument for trying to be a good neighbor to Meta, because you can always, always be sure that Meta has no concern for being a good neighbor to you.