No, it can’t. In order to be able to create a new version, the file has to be uploaded through NC’s APIs. If you operate on an external storage, or even on NC’s local data folder, bypassing NC’s APIs, then NC simply doesn’t have the chance to copy off the old file to a new version, before the new file gets placed onto the storage.
To make it simple: if you want to rely on NC’s version control app, you will have to only use NC’s tools for uploading or changeing files on the storage.