I always felt like the ultimate flow with Slack was to make focused channels for a given topic; threads are too generic and hard to track and I generally get the impression that they're meant to be ephemeral, whereas a focused channel will of course ensure all participants know the intent of the channel, and the content is not lost. Essentially, a channel should be treated as an e-mail thread. Once the topic has finished, you can close the channel and archive it for future reference.