Hey! So, a root NIP-05 is when you are the 'default' or root profile in the NIP-05 domain. For example, if your NIP-05 is negr0@hodl.ar, the root NIP-05 would be _@hodl.ar. Notice that the underscore represents the default or root value of the domain. This typically indicates that the user is the owner of the domain, which can have some presence connotations. In the case of Relatr, having a root NIP-05 is just a way to slightly increase the score in the case you have a valid NIP-05. On the other hand, the reciprocity metric determines if the source pubkey and the target pubkey follow each other.

nostr:npub1th6r23tltjuy6r498z90hlg092yx0ddk5a700xdkytdqjgfhmrysceymrz uses the default instance of Relatr, so the source pubkey from which the trust is computed is determined by that instance. The default instance is accessible from relatr.xyz

Hope this clears up some doubts. Feel free to ask if there's anything else we can help with.