Notes & replies can and often do get published to different relays. Primal probably has everything because it's all cached and it only reads from there. The replies probably show up in other clients because they're also present on other people's relays.

phenixfalconer has a bunch of dead relays (and a couple I can't connect to) in their relay lists. The Primal relay might be the only live one he's using, and maybe the primal relay is failing to relay as expected for some reason, as I see the same thing.

You can fork it into an nsite and make changes to the base client, too so that it suits your needs better

If I'm understanding correctly, I think https://hallway.fiatjaf.com fits your requirements.

Anytime.

Anyone can be banned at the relay level, blocked at the client level, or muted at the user level. Nothing prevents the banned person from publishing to different relays. No follower of that person would know if the client was blocking, until someone else they follow who's using a different client, somehow makes it obvious, via reply to blocked user or a statement about it... unless we all get comfortable with the idea of using multiple clients, which I think and/or hope is already the case for the majority.

I wouldn't consider the above to be shadowbanning. That term, to me, means a post is completely visible but somehow otherwise suppressed, like prevented from appearing in a trending feed or something. Those posts are blocked at the client level and require the reader to adjust security settings to see them. Fortunately, Amethyst supports such user controls. Other clients may not. (Not that this is a problem now, but something to be conscientious of, in the event that very opinionated clients become popular and some person writing extremely contentious notes appears among the crowd.

App.flotilla.social
Wisp.mobile

Understandable! It is good to be cautious & test, especially with signers.