New user here.
In answer to the first question, I think the answer is that you can't. It doesn't seem to have been integrated in that direction. I think the design is for end-users and end-devices, not the servers, though seems like a really easy thing to add.
As for the second question, that looks really strange. I can see why it might show up on the actual port as well as a port channel (Po11), a router interface, a bonded router interface, and several switch uplinks if it hits them before it gets to the router. In my environment, I do not watch the router interfaces or the uplinks for this reason. However, I have seen similar weird things where I found my laptop at remote sites that I haven't been to in a week but it shows I was there yesterday.
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I think it would be a feature request. However, I would check first if you have NPM as NPM is the one primarily getting those topology information. If you only have UDT, I'm not sure if it does pick up the whole topology. It only concerns itself with Endpoints connected to networking device.
For your second question, What I'm gonna do here is to check the MAC address table of those devices that shows that Endpoint as indirect. If it appears there, then it would be picked up by UDT.