I don't understand. You can configure your node module to use specific versions of libraries just like a C project. Surely you've heard of problems people have with dynamic linkage and their programs not working? This is why distros spend so much time getting things to work with each other - I think you're just sweeping that under the rug.

The tools you're working with aren't different on this manner - it's not like your tool will magically recode itself to work differently.