Yeah, I agree on all counts. Also, if it's a really good spot for a city, people are bound to go back there eventually.Don't get me wrong, it's a really exciting piece of research - adding to a growing corpus of evidence for long lived and widespread complex societal settlement in the Amazonian basin. Just saying that the abandonment of these settled landscapes has nothing to do with European diseases like smallpox.
Also, while cities are relatively commonly abandoned/fail, they're also frequently incredibly long lived (whether continuously or in waves of resettlement and rebuilding), so when a previously (relatively) densely populated landscapes is pretty much completely abandoned (as is the case here, or as seen in the southern Maya Lowlands) it's actually quite unusual - which just adds to how interesting this all is!
It's just a pity there are not more written sources (or maybe: not more understanding of unusual writing systems!) for South and Central America. Purely archaeological sources can only get you so far in understanding historical chains of events - and of course when all you have is LIDAR imagery, you really have next to no idea.
Is this a subject you've studied more? I'm really an absolutely layman in this.