I still don't think search for public posts needs to be opt-in. But even ignoring that, my point was that mastodon merged this change without coordinating with other projects. They didn't check what the easiest way to signal an opt-in would be for other projects. They made the decision unilaterally and now other projects will be left out of masto search by default. And if their users want to be searchable from mastodon, they have to stop working on features for their own project and work on this.
My issue is just that mastodon never respects other projects enough to coordinate, makes decisions that affect other projects without input from them, implements features that further isolate mastodon users from the rest of the fediverse or makes it harder for them to interact.