Well, it certainly could screw you up, because you're putting the sub "in a corner" by setting it on the couch. You're artificially directing its output, so the exercise probably doesn't accurately approximate the room nodes. I don't think all the damping could "help", either.
If you could set something sturdy between the couch and the sub, that might help. Even if the sub is "too high", you'd still be measuring the bass at your head at that position (or something). You might also try orienting the sub in different directions.
