What are you expecting to happen when your users access you AccessPoint.
- The Windows user name should appear in the Welcome User in case the WebServer is using NTLM (single sign-on with the user windows login account).
- The user should be able to see those documents for which he or she is authorized (in your case as you're using NTFS as the authorization security mechanism they will see only those documents in which they are included on the windows file permissions).
- When a user tries to open a document on the AccessPoint the Section Access is applied either checking the NTNAME either asking for user and password.
The Section Access is a data security mechanism, not an authorization mechanism, so that's not something you can replicate.
May it be that you want to rely the authorization mechanism on the section access of your documents?.
In that case, in your scenario, the only option I can think of is to authorize every user in the system and use the "Filter AccessPoint Document List Based on Section Access" option that you may find at the bottom of the Server tab of the Document Properties.
Using that, every user can potentially see very QlikView application on the AccessPoint, but only the applications in which the user is included in the Section Access will appear.