The argument is that the popularity of the layout in contexts where it's possible is a strong argument for enabling it on the web as well. This is not a layout that they just thought of and are trying to invent.
Row-less layouts with columns are indeed quite common in the non-web world - see for example newspapers or other dense text. But that can already be done with current CSS features, and the row-first placement makes this proposal completely unsuitable for that. Masonry actively makes that worse, because it screws with the regular reading order.
They argue that nobody is doing it because it can't be done in CSS. I would argue that nobody is doing it because it's a bad idea. We've seen people work around it not being in CSS by using Javascript to make galleries for years now, if there were other use cases they'd surely have done the same?
With the exception of Pinterest-style galleries (and lets be honest, that's not exactly the pinnacle of UX either) I really don't see a widespread use for this feature. Their three other demos sure aren't convincing me.
Honestly, I'd say kudos to the WebKit folks for opening the discussion and being transparent about the process and the tradeoffs. It can certainly help refine (or inspire) future proposals.
It's obviously not viable to implement literally every single design imaginable straight in CSS. If I want to do something silly like placing my content on the faces of a hypercube it wouldn't be realistic for me to expect that to be part of CSS. Having me write some JS is completely acceptable - that's what it is for, after all!
It's not a matter of "would this be better in CSS", the answer to that is painfully obvious. The relevant question here becomes "is this common enough that it warrants a CSS implementation". And honestly? In the case of Masonry I am not convinced it is.