I have submitted bug report DNNP-5887 for this. Here's the detail on what occurs:
Here's an example of what happens in v 4.4.1:
(Assume all portals listed below are in a single install of DNN.)
(1) Username BOBJONES registers in portal1.myportals.com with password of bobby. All is OK.
(2) Username BOBJONES tries to register in portal2.myportals.com with password of golfer. This errors out with a username already exists error. This is OK in my opinion.
(3) He now tries to register as BOBJONES in portal2.myportals.com with password of bobby. It allows the registration, but he is not assigned any roles (not even Registered Users or Subscribers), so he has no access to portal2.myportals.com.
(4) I log in to portal2.myportals.com as the admin and try to assign a role to BOBJONES. When I click the Add Role link, it simply flashes and comes back to the same screen. No role is assigned. My custom roles have the same names in all portals, but so do Regsitered Users and Subscribers.
If it's going to allow the registration, then the user should be able to get roles assigned automatically and manually.
FYI: The security guide in the DNN docs says that this scenario is supported in the data model but not by the user interface, so I assume it was never meant to work. If not, then the validation routine should block the registration in the first place.