So, slight correction to my previous post (which I now deleted) thanks to @troplin.
It seems that phrasing content like <span> elements are allowed inside <pre> elements according to the spec, so Lemmy is actually doing the right thing there. It's on kbin to fix this, not Lemmy.
I commented on one of the closed issues about this on the kbin code repository, asking for the issue to be reopened. Hopefully it will so this gets fixed, I'm not sure though how visibility works if the issue is already closed. I'll make a new one if it's neither reopened nor replied to until next week, if no one else does first.