You could use what I used when I had the same issue with Dropbox. And that's to use: NTFS Junction Points like you said.
It's pretty much a worm hole in the file system that makes a shortcut without appearing like one to applications. There are downsides to using these as an antivirus would scan both folders (despite physically being the same), amongst other things.
Try something like Junction Link Magic instead of command lines if it helps.
Update: it appears JLM does not create junction points the way we wanted. Instead use Junction Master which creates hard links, and that will lie to applications the way we need it to. You can read more here.
Creating a link in Junction Master will allow Google Drive to see it in the options.
If we look at it in terms of shortcuts, consider a Junction Link as the shortcut file, and Destination as the original location.
And consider looking at tutorials to do this for Dropbox, as Google Drive similarly has only a single sync folder.
Oh and I'd avoid juntion points between drives!