I have had similar experiences, but not on professional context. Random E2EE key issues (not often) that maybe sometimes resolve themselves or with some additional action like bringing all clients online. Matrix is still the best choice for me, though, and I expect it to improve like it has over the years.

Last time I tried the threads-feature (with Element) maybe a year ago, it was still in beta.

Anyhow, if you're ok with Slack, then you probably could have just not use E2EE at all and avoid issues related to that?