I think that's a very reasonable thing to complain about in the context of dependency management. The runtime (node.js) and it's compile time + run time options

I think that's a very reasonable thing to complain about in the context of dependency management. The runtime (node.js) and it's compile time + run time options are actually a dependancy of your application. As an end user, I shouldn't be expected to know how to configure x dependancy for my system to run y app and as a software developer I shouldn't have to build / package apps to match the client's system configuration. The sticking point is (back to my point) that the vast majority of distributions don't give the app a way to manage the deps and get specific deps in required, the best you can do is list x as a dep in your package and hope that it won't break your app or the system in some way.