Non-profits are not an antidote to corporate control. Non-profits rely on grants which are typically coming from corporations or governments, with strings attached. While there are a handful of legit non-profits, the majority of them are just ways for people with money to burn to expand their influence on various issues. Especially when they are focused on setting standards like this, as opposed to turning donations directly into meals / supplies / shelters etc.

There have been discussions of doing this on Mastodon as well, but they have been met with resistance. There are several instances which have incorporated themselves as one form of non-profit or another (depending on jurisdiction), but the centralization of block-lists or introduction of federation-wide governance bodies has not taken off for various reasons.

In general, it is good practice to look at the block-lists from a few instances you vibe with and use that as a starting point, but realize when it comes to politics, everyone is a crank and that simply copy/pasting their lists isn't the greatest approach. A lot of instances are shit and belong on those lists (the bigots), but several end up there because people are allergic to nuance, while several are omitted because people think a subject is nuanced when it really isn't.

Also, I wouldn't worry about an instance getting too big at this stage. Some communities are big. Some communities are small. Some have irreconcilable differences. As we stumble upon these differences, there will be splits. New instances get started up every day. People will have disagreements about the way admins / mods handle things. This is how it goes. Having 100,000 homogeneous instances of equal size does not indicate a healthy network. The way these things split and group up is driven by culture and politics. The ideal place to land has nothing to do with the size of the instance, but your trust that the administration won't cleave your community in half for arbitrary reasons.