I just installed UDT.
I found that the same issue was present.
I do NOT let NPM or any other product "auto-discover" the network. Besides, it seems that one product does not rely on another for the very same db information already present.
So, what I have done and did for UDT is do the "Add ports from existing ORION Nodes".
There you get to select the devices from all of the Vendor categories etc.
I simply added a set of Nodes from that point and let the software go for it.
I will caution you that if you import a lot of nodes at the same time, the response time will be slow for the other apps running (NPM, NCM, NTA, etc.).
I suggest that you import a group at a time to eliminate a heavy load on the server(s).
After you get the ports into the system, I suggest that you go through your network and determine what ports are really Trunk Ports. select the ports that are TPs and "UNMONITOR" those. It is cumbersome but, well worth it.
DO NOT "UNMONITOR" ports that connect to Cisco Phones. Those phones can and probably are, used for connecting the phone and a Computer device of some sort. UDT and the phone will correctly identify these as "Trunks" even though they are defined on your switch as "access" type ports. You will see two MACs and at least two IP addresses. That would be correct.
The same would be true for Wireless APs that are attached. There is no need to see the switch port unless you want to see all of the MACs and IPs where the AP will diplay that information anyway. Again, you may want that to track how a device goes from wireless to switch to Trunck, etc.
That should get you started.