I think I am OK with the idea that replies to the first post, that don’t quote any part of the first post, should be considered general replies to the topic.
As I already pointed out, functionally they are already identical anyway. If you reply to someone’s topic, they always get notified – whether you mark your post as a reply to the first post (click the reply action on the first post), or just as a reply to the topic (click the reply button at the bottom of the topic).
So we can probably suppress the “in reply to” chicklet at the top of the post for these sorts of replies, as a default, for all instances. It can be a setting too I suppose.
(This will be a much worse problem once BB switches as planned to the first post being a Reddit / Hacker News style link with no excerpt whatsoever. Seeing “In reply to” on replies to the first post there would be utterly pointless in that scenario, even more so than it already is…)