I am thinking that the net reduction of oxygen molecules due to pulling a vacuum would have an almost negligible affect on the stability of the honey. Perhaps the payoff is more emotional than measurable.
The steam from hot pressure canning is a different situation where it physically displaces all the air above the liquid before the sealing takes place. It need not reach a high vacuum in the eventual sealed space. This steam displacement of free oxygen does not occur unless you want to thermally degrade the honey.
I think the OP is concerned with sealing more than preservation. I just torque it every time I handle it. I guess you could dry heat the lids to soften the rubber. They would cool before any damage could happen to the honey.
Of course, mine often get to ride in a car in the texas heat to soften it.