I believe that it is not currently possible to disable update notifications for particular nodes. I am using a hacked fork of a node, installed directly from github. Since the version in npm has since been updated then I get an update notification for the node, which I want to silence.
If I remember correctly, the update notifications respects the node installation/update exclusion list. But I don't remember if adding the node to the update exclusion list (denyUpdateList) will remove your fork.
There's also the versioning; I remember working on it, but it's still on the very long list I'm giving to Nick
You are missing the point. If I decided to revert to the published version then I would uninstall it using npm, then install it again. The issue then is that I would not get any notification if the author updated it. Even in manage palette I would not see the update.