What we have is the natural way to do things with web stack (the way it's is mean to be used), and the "hacky way" (the way that let us do what we want to do, even when the web stack doesn't support it yet).
SPA is the hacky way today, but before it we had CGI, Java applets, Flash... And the web purists were always very vocal against the hacky way.
But the hacky way is what pushs the envelope of what the natural way can do. Every feature cited in the article that makes an MPA competitive with an SPA today only exists because of SPAs.
I'm on the side of preferencially use the web the way it's meant to use whenever it's possible, but I love to see what can be done when we are a little hacky, and it's awesome to see the web stack adapting to do these things in a less hacky way.