As you noted above, Discourse discourages sprawling tree-like explosion of discussion by maintaining a (rough) top to bottom flow.
With some lightweight moderation (like Brett’s split of the vote date discussion from the big Python Governance Electoral System thread) you can achieve better threading in ways that mailing lists couldn’t properly handle before (off-topic discussions about e-mail clients on the Timeline to vote for a governance PEP python-committers megathread are a great example).
In other words, you can split off messages after the fact to provide a better linear flow for everybody to enjoy. In a way then this is more a matter of proactive moderation of hot topics, rather than an intrinsic tool deficiency.
To flip this around, I think that Brett is simply saying that the benefits of threaded views in e-mail only apply to a subset of e-mail users. On the other hand the problems stemming from immutable tree-like explosive threads are universal.
In general, the next generation of Python core contributors is increasingly less likely to be e-mail first, let alone Thunderbird-first.