In terms of when you would use the Management API v node.js version. I think it depends on your use case. For example, if you have a custom API backend or regular web application say written in .NET for example and your want to provide users with the ability to modify their user_metadata properties then this may lend itself nicely to calling the Management API directly.
Another scenario could be, if you have a backend service that runs on a schedule via some task scheduler, this may require an application that can execute on the command line and in this case the node.js offering might lend itself nicely here.
There may also be instances where the node.js npm package could execute over web if you have a node/express application and the Management API could be executed by a console app so it could just be a question of best for the job or even preference for one over the other.
The bottom line is, both options are available and you choose whichever fits best your use case.
Warm regards.