in Matrix’s case it’s a big roadblock, as the main Matrix server hosted by Matrix themselves has unfortunately become the defacto main server that most people use, which means not federating with it massively reduces the ability for someone to just be able to seamlessly hop onto your server unless they too are on one of the smaller, less popular servers.

Maybe. But on the other hand, Matrix is only just beginning to become known among gamers, and there are a lot of us. Seems like a good time for people to stand up a new servers and invite the gaming masses.

it would likely be a bit of a deal breaker if you met someone in an online game somewhere, and then invited them to your self-hosted Matrix server, only to discover they are on the main potentially israeli intelligence-tied Matrix instance,

I've seen occasional claims of that for a few years now, yet not once have I seen any credible evidence of it. Not in their own weekly reports. Not from journalists. Not in spec drafts or issue trackers or organizational structure. Nowhere. This particular legend smells more like fearmongering to me. At the most, it looks more like the distant connection that the internet has to the US military: Sure, part of its origin story might have been there, but it's not relevant any more.

(Also, if your goal is to avoid Israeli intelligence-tied people seeing your room meta-data, you probably shouldn't be inviting strangers to join. After all, there's no way to know who they really are, regardless of what homeserver they use or what chat platform you're on.)

For what it's worth, account portability (giving people a way to switch homeservers) is on the Matrix roadmap.