We have a multisite installation with multiple networked sites and created custom roles and have more or less removed almost all standard roles (only admin and subscriber remain).
When we add new users, we will always apply more than one role. So when we go into a site in a network and add a user (Users -> Add new), besides “Role” setting we are also adding roles to “Other roles”.
The issue is when the user is saved, the other roles never applies to the user. The new user will only get one role and we have to wait until the user have confirmed the account before we can fix it.
I missed this topic somehow. My apologies for delay with response.
The recent clarification is very important. I missed during development the scenario with user account activation via link sent by email and tested only interactive user creation by admin without confirmation email involved. So look at this part (activation of account with multiple roles via link from confirmation email) as a feature, which is not realized yet. I will add it definitely. I will try to make it with the next update.