There's a very large segment of the mastodon population that thinks servers ad big as .social are very bad for the ecosystem. A lot of instances defederate them out of principle.
The argument is that .social is so big that it's not possible to moderate effectively. It also presents a very large and inviting place to launch attacks from. We frequently see waves of spam, abuse, and just bot accounts originating from .social.
A lot of severs are already defederated from .social for these reasons
Would you also know if it's commonplace for instances to deny by default, and then use whitelisting?
The fringe-er instances are more likely to block by default. It's almost an issue of fediverse fundamentalism. A lot of people think large instances like .social are antithetical to what mastodon is trying to accomplish. We have huge, enormous centralized servers in the middle of a decentralized network. I think you can see how that sentiment would come about