I don't fully understand the whole instances thing, but I know if I make an account on startrek.website's instance, I can't see a lot of other instances that I can see when I log into an account I made on, say, lemmy.world or lemmy.ml. Is there something that mods need to do to enable this, or is this a purposeful decision to stay unconnected to non-Star Trek related instances? If that's the case then everyone will need to make another account to view this content, which creates a lot more friction and would limit the odds of achieving critical mass.
There is more friction when you try to subscribe across the fediverse, yes. When you subscribe via federation, your home Lemmy has to pull the content in. (This is an interesting view, as far as I can tell its all the communities that accounts here have subscribed to.)
On some level the best approach would be to put your account on a big Lemmy so all the communities there are preloaded from your account, while you still have the option of subscribing to communities on other Lemmys and pulling them in.
That said, there are already apps and browser extensions that manage this for you with Mastodon. Here's one example. This just makes it so "Subscribe" buttons on other Mastodons work by doing the extras steps for you. It's only a matter of time before utilities like this start materializing for Lemmy. (They may already exist.)
I didn't grok this is how federated subscriptions would work before joining here (although in retrospect and as a Mastodon user, it's obvious) so like you I'm a little bummed out. But upon further reflection, I'm good with dealing with these inconveniences until extensions, apps, and Lemmy itself starts to alleviate them in software if it means I get to beam into other Lemmys as "GuyFleegman@startrek.website."
I'm in the Sopuli instance and I can see this content fine. Although it seems you might be talking about the reverse, you can't see other instances with a startrek.website account?
Gonna do my best! Right now this community is having some trouble downloading posts/comments into the one I belong to, I'm hoping that's a temporary glitch.
Things look like they're up and running smoothly now. Comment numbers now appear to match across both site views. I'll periodically check over the next few days and see if I notice they get out of alignment again.