If you use email for login in the mojoPortal site, then the user email address will already be in the identity cookie and can be obtained in mojoPortal code by Context.Request.Identity.Name, so maybe it could also be obtained within the other app in the same domain.
There are some reasons in mojoportal why we don't want the user name to be the same as the email, thats why we replace the @ with .
I could possibly implement a plugin system for user login event similar to user registered event so you could run some logic that sets extra cookies that are easier to track from your other app. Let me know if that would help and if so I'll try to do it in the next few weeks.
Hope it helps,