A little confused. When you use L6Link, it sets the POD output mode to 'combo power amp' and the L2 to electric guitar mode, which seems to imply that's the Line6 recommended way of using them together. Doesn't that defeat the point of a full range flat response system? The speaker is coloring the sound and the POD is expecting that coloration so is altering its output to suit.
Also, if you're using the L2 as backline and sending output to the soundman from the pod you'll want to have the pod in 'studio' output mode. Problem is them you'll want the L2 in FRFR mode, meaning you can't take advantage of the groovy virtual tilt back thing. If you put in keyboard mode (for example) what you'll be hearing will be colored and different from what the soundman gets, no?