Edit: obligatory explanation (thanks mods for squaring me away)…
What you see via the UI isn’t “all that exists”. Unlike Reddit, where everything is a black box, there are a lot more eyeballs who can see “under the hood”. Any instance admin, proper or rogue, gets a ton of information that users won’t normally see. The attached example demonstrates that while users will only see upvote/downvote tallies, admins can see who actually performed those actions.
Edit: To clarify, not just YOUR instance admin gets this info. This is ANY instance admin across the Fediverse.
You are right. A solution that would keep messages secure and hidden from an instance admin will have to use a solution that’s not under the control of the said instance admin, and you might as well just use PGP for that manually. But now I’m wondering how does e2e encrypted services such as Protonmail do that, so you can be sure that they don’t have access to your data. I’m assuming there can’t be any guarantee, unless you have your keys separated from the app and do your encryption before you let the app touch it.