I want to reserve my vents about database ignorance to situations where it really makes a difference. This isn't one of them.
While I think the tree structure of discussions is useful, when used appropriately, it's not as important as many other things in the overall goodness of a BBS. And the upside of "Quick Reply" is that, to the extent that people use it, it provides a consistent behavior pattern, even if it's a wrong behavior pattern.
The regular readers will adapt to the odd tree structure. In Ezboard/Yuku, that's already happened. Regulars, including you and me, make it a practice to preface their remarks by something that will establish the context of the message being responded to. This allows the reader to mentally reconstruct the "logical tree structure", although no readers probably think of it in those terms.
They would have done better to inherit the title (adding a "RE:" when necessary) from the same post they choose as the parent of the quick reply.
That's an opinion, not a vent.