The extra column next to the one I'm reading introduces a lot of visual noise, and the content is hard enough as it is. I'm sure physicists have all gotten used to it, but it certainly trips me up.
Papers are generally not read start to finish in one go: there's lots of rereading and jumping back and forth between key parts, and anything that moves them further apart makes this harder.
I still think a flexible layout is best. If you like multi-columns and have a wide screen, why not display 12 columns next to each other?
With PDF this is not possible. With HTML the content can in principle be sliced and diced how you like it.
But HTML is so much more flexible, and ideally people can choose how they want it, although at this point it seems that's not (yet) implemented.
I find jumping back and forth is always a pain on computer screens and ebooks by the way, and is the major reason I much prefer print for this type of thing.