> how you manage/compose them in one or many of your apps without embedding multiple times the ScalaJs runtime
That doesn't make sense. You have code, maybe also dependencies. Scala.js compiles it and produces one JavaScript file with a single runtime and only the bits and pieces of your code and your dependencies that were actually used.
> Don't forget Scala is slow to compile and ScalaJs is even slower so if you have a monolithic js app it won't scale as a good developer experience.
ScalaJS incremental compilation is so fast that it's already done when you switch from the IDE to the browser.