@maloki Right, that thing could probably be fixed by doing a remote-fetch of parent (which I believe #Mastodon does for replies to unknown posts, right?).
I haven't checked whether the feed is fixed yet (@Gargron mentions the Suprrrfeedrrrrr "sanitation" with thr:in-reply-to)
We stitch together instances in !GNUsocial based on the conversation URI though, which is never stored or distributed from #Mastodon (which relies entirely on thr:in-reply-to)
What we have is however a bit of a mess and I don't remember which part is what we actually use and which part just comes along from #StatusNet (where none of this worked and conversations were even more broken).