If you change to use email address to logon, from the username sign in ..
2 scenarios where you will run into problem if you have multiple portals on 1 DNN instance.

1. A user is a member of Portal A, he can not sign up for portal B as his email is the same. He has no idea you run both portals.
Reason, the email address must be unique in Asp.net membership not just portal. Good luck explaining to Portal B owner that Portal A is more important, therefore the user can't sign up.

2. A user was a member of Portal A and B (you used username sign on). You switch to email sign on. You need to set require unique email or the password retrieval won't work.
If you set require unique email = true, the admin or host can't log into site anymore. You get a warning, check your event viewer. Funny, you can't log on to check event viewer.
You need to set unique email to false so you can log on but now the pw reminder don't work.

How can we make this 'unique email' for portal level only?

One of the duplicate emails I found was a user login into Site A by first registering as a user and later login in with Facebook. It seems DNN treats them us 2 different users but they have the same email.