As a package author you use whatever you want (rollup, webpack, gulp, grunt, ...), but you will most likely publish to npm, because bower is dead.

As a consumer you use npm or yarn, it doesn't matter, and a tool that handles modules, probably webpack. Even if you'd use something else (rollup & parcel come to mind), it doesn't matter, they will all treat your dependency the same.

EDIT: Yeah i just saw you're referring to Polymer. I take it back, everything you said applies. But then again, people probably want to suffer when they use it. Though very few actually do use it. I just don't think it's a good example to make to describe web dev in general. Rather Google was the only one that missed the train it seems, they worked in the opposite direction.