They do charge $3000 for some of their journals (although the flagship is $1600 as you say). The waiver is probably the more important bit here. It's not hard

They do charge $3000 for some of their journals (although the flagship is $1600 as you say). The waiver is probably the more important bit here. It's not hard for me to imagine that a professional high-quality academic hosting service costs something like what PLoS charges. Their budget is probably publicly auditable. I work in enterprise software, though, so I've become kind of inured to seemingly absurd costs for technical solutions. I used to work in academia, where I became inured to PIs spending crazy amounts (millions per year) on equipment and lab services, which makes me think $1600 for a publication really isn't that big a deal for most developed-world STEM labs. Although I'd rather they spend it on making post-doc salaries livable.