Another thing I noticed is that lots of people just skim their feed and respond to the top note, directly, rather than reading the replies.

Which means their responses are often nonsense.

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Personal experience though, here as well as on the Fediverse: How the whole thread looks like can vary pretty much depending on ... random factors beyond actual users control.

That's true. Other than Amethyst, it can be very hard to see the full thread.

Yes, also so far found Amethyst to practically be the only tool here that works...

I think it's also the only client that rolls up the reply count, so that you can see if there are already replies to read.

It's ahead by a mile, IMO.

Not always, sometimes some relays don't show all the comments or comments can be seen after some time etc.

Yeah, that's why I cough up the dough for the wine filter. Used to drive me nuts.