I figured it out. Since the inlet and outlet lines of the cooler are at the bottom of the transmission, one would always get the right level filling up to the fill plug regardless of if you drained the lines or not. Draining the lines does get all the fluid out but I don't think the amount of old fluid in the lines will do any harm long term. It will all get drained eventually with multiple fluid changes. Please correct me if I am wrong!
I am still confused about draining the transmission cooler lines. I have access to DIS so I will be draining the lines but I am trying to understand the logic behind getting an accurate oil level. As someone pointed out, in theory aren't you overfilling the transmission if you aren't draining the lines? And vice versa, if you are filling the transmission till the fill plug after draining the lines, aren't you under-filling?