I really don't understand the confusion.
Incognito prevents the browser from remembering the things you do locally to the browser itself. The browser, any browser, cannot control what the server does. The browser cannot block whatever javascript you have allowed it to run. All it can do is block javascript. You log into a server while in Incognito doesn't mean the server won't know you logged in (wtf?).
Icognito basically means your SO won't see your browser history, and that's about it.