Electron apps' Chrome stores its cookies separately from the user's installation of it, correct? That, plus the lack of a logged-in account within Electron's Chrome might help to mitigate user cookie correlation and the like, right?
But Electron app has full access to your system unlike normal web page. So it makes sense to run Electron apps from separate user account so that they cannot read your browser history, cookies, install you an extension etc.
I wish someone with a lot more knowledge than me on this replies. You raise a very valid, practical and useful question, would love to hear the answer :-)
Not sure about in-browser IP tracking, though...