"Thread-first communication" - We have it. Email threads. I've been using Zoho Mail. It's one step ahead and has modern concepts like streams/commenting and sharing built around emails. Very useful.
"Truly transparent conversations" - What this means is, the knowledge has to be highly searchable. Also, not all threads have to be public. With emails, you can either broadcast an email company wide or you can opt to pull in relevant users into a conversation. Makes a lot of sense to not broadcast everything company-wide, isn't it? More importantly, emails are easily searchable. Once received, I'm confident that it's going to sit there in my inbox forever, without worrying if it's going to be deleted later by someone who has authority.
"Leaving out the online presence indicator" - Exactly. Emails.
Maybe there's some more important key aspects that the product's covering up for me. As for me, I guess emails are simply good enough!