I run my own, and have seen no trace of this being "presumed evil" you speak of.
What if I want to be on both? Well you need two accounts.
Also you could always host your own instance and be your own admin. I started doing that a couple of weeks ago. It's easy to find a host plan, if you don't want to do all of the work yourself. But you could still do that if you wanted to.
That schism is inevitable. To pick an extreme case, imagine a server for LGBTQ people and another for self-declared neo-Nazis. The people on the 1st might have very strong feelings that they want no contact whatsoever with people on the 2nd. There’s no world where it’s reasonable to say they have to keep their servers connected.
Now suppose you want to follow people on the 2nd server for journalism purposes. It’s unreasonable to have an account on the 1st server and then complain that they’re not talking to the 2nd. Even if you have legitimate purposes that aren’t creepy, they’re not going to go along with it. So instead, you get another account to follow the 2nd server and everyone’s happy.
The Mastodon server I own turned 7 years old today. We’ve blocked probably a couple dozen servers over the years. In every case I can tell you exactly why we blocked that instance. Most of them involve, literally, their users sending mine swastika imagery, death threats, or other utterly indefensible content, and the moderators of those instances being OK with it. My users stick around because they trust my explanations for the moderation actions I take. They don’t want to manually filter actual Nazi content from their timelines. Those that do can pick any number of servers that wouldn’t block that content.
That's a feature, not a bug. Whatever your preferences, there's an ActivityPub instance with moderation you'll like. Want to be in a liberal thought bubble? It's there. Want nothing but all Trump, all the time? They have that. Only the good things about astrology? Yep. Aggressive blocking of anti-science woo? Sure.
Moderation decisions are made at the instance level, not the network level. There are instances that take a laissez-faire approach. Others are quite heavy handed. Most are somewhere in the middle. Users can pick which sounds best to them and find servers that align with their wishes.