If I have a library (libA) that uses fooV1 and another (libB) that uses fooV2, there is no reason I should expect those two dependencies to interop with each other (except explicitly stated by the developer).
The solution (that there should be one set of dependencies) is an even worse problem that currently afflicts the Golang community, which they have decided to solve the same way npm has decided to solve it - vendoring.
Now with Golang, if you only have 1 set of dependancies, and one of your libraries depended on an older version - your program just won't compile (unless you update the library to use fooV2) and I'm not sure how thats useful to anyone. Most people will just tell you should have have just versioned that dependency.
1) Windows' limit of 260 characters per path name is incredibly small for a modern OS and that was true many years ago as well.
2) Npm approach relied on well behaved OSes and file systems allowing long path names. It's not future proof because you don't know on which OS and file system you'll need to run, maybe some limited embedded device.
Ruby's rvm solved that problem with a single directory level and a gem@version naming scheme.