Are you sure the users are consuming license twice? I would expect both licenses to be available to the users with the overlap however the user would always be using the User Access pass.
In the case of User Access being assigned to the user and no one else can use it. However in the case of login access a pool of user is assigned to the pool of Login Access passes but they are only consume on demand/when needed.
What I would expect to happen is the Qlik Sense would check if the user has an available User Access and if not then check if the user is in Login Access pool of users. By doing it this way the user who has a User Access would never consume a Login Access pass (unless the user's User Access pass is removed of course).
i am pretty sure because as I am the only user for now - i just installed sense and did not enable it for other people at our organization. I saw my windows ID on a license dashboard twice under user access license type and login one once i enabled both license types - login pass was assigned to one AD group and user pass to another one and I happen to be in both of them and already had user license activated for my account so i did not expect to consume login pass.