This is covered in the User Console Install Guide actually. In the 5.5 version its on page 47. The item marked as a solution covers most of the steps but misses the small changes needed to a NBI.configuration.config file.
This is certainly possible and has been done for several clients. Its just configuration within IIS for the correct auth. Flexera Services can speak with you to assist to get this setup right for your auth method and smart card particulars.
It updates the Normalized_xxx fields and keeps the original value. It also setups different default views that show the new normalized columns/fields (since those are obviously better), but the old ones should still be there.
Glad you have a ticket... For anyone experiencing this install issue please work with support please to dig in on your authentication setup as well as if you can just flip the installer flag on that step that its stuck on.