Thanks for the reply and the link, it was a good read. I'm away from my setup for a few weeks but when I get back I'll plan to use the pad to prevent overloading and set the impedance to 3.5M ohm as i'm on auto now and don't want to darken my tone. Might even record some A/B's of guitar to guitar in on HD500x VS guitar to DI to mixer to guitar in on HD500x and see if it makes much of a difference and report back.
Good tip about paying attention to the doubling up of identical inputs - i would have expected line 6 to reduce the levels if the inputs were the same rather than always summing, but always summing is fine as long as i know to set the other input to something else. Overall I doubt it will make a dealbreaker difference tonewise to feed the guitar input directly vs through the mixer aux.