My take when building was this, until the wings are on the plane and rigged to the sticks, you can't measure down travel.
With wings on the bench, all you can do is set neutral and possibly check up travel. The up travel stops dictate down travel of the opposite aileron.
I haven't been worried about the push rod tube making contact. Mine does, but by my estimation the down travel is more than enough and the stops will in fact stop it at the correct location before the tube makes contact.
Seems ok to me.