As he said, not an issue, don't worry about it. Having said that, if you are using soil that is not so well drained, elevating the pot a bit might help with aeration of the lower pot.
My autopot grow did just fine with the bottom of the fabric pots in liquid most of the time. The autovalves allowed the medium to drain with each cycle, but the bottom of the pot as well as ~3" of the lower pot sides was seated against the plastic, and I had healthy roots throughout.