Hmmm The manual also says that the 2:90 needs unshielded cables to activate the modern, deep, and half gain options. Not true and MESA reps say either will work, plus good luck trying to find an angle-to-angle 6" unshielded cable.
Same with the line/ instrument switch, MESA says either will do, as long as you are not overloading your 2:90 with too much volume or input. Use your ears and decide what works best for you. I tend to use it on instrument to get the better noise to volume ratio, more like a rectifier head. I keep my output at 3 on the Triaxis and turn up my 2:90 to about 3-4(If it was numbered 1-10) and it is plenty for me to rock out any LA venue or arena.
I also sometimes run an a/b/y switch into the Triaxis and 2:90 for a layer tone (a and b going at the same time on the switch). Using both channels of the power amp at the same time. So one channel is actually straight guitar input and the other is coming from the Triaxis(line). So I just keep the switch on instrument and it works well.