I think what you are talking about is instances that may have a large population of marginalized groups, and the fear that someone is creating a database that could be used to easily seek them out and use it for trolling and such. Which I think is a very valid concern.
And as mentioned above, you have the crowd that wants to take an instance and give all their posts over to for-profit corporations like Threads and Bluesky, that should not even be called part of the fediverse IMHO.
I don’t know how you make a global search for the fediverse that avoids both of those issues though.