I pretty much go at it the way Mike described. With a few bowl forms that I make often I actually do finish the foot at the same time as the outside profile and make it exactly the right size with just the right sized bead or groove or something for a jaw set to fit, so when the bowl is reversed to finish the inside the foot is not dinged up at all, even though the jaws are gripping it pretty tight.
It saves another reversal to do the foot which is a time saver in a run of utility bowls that are headed to a kitchen store or whatever.
Mike's right though, it's not good to get locked into a design corner by the size of the chuck jaws, but if I was going to make the foot that size anyway, well what the heck.
I have tried to protect the wood from being marked by the jaws, (rubber pads, tape, rags etc)which happens when the tenon is a touch bigger than the true circle size of the jaws, the corners bite in, but have not really found any way to do it that I was comfortable with. Anything that was stout enough to actually protect the wood always felt a little unstable to me and introduced vibration that I didn't like.
Nowadays, when I want a foot that's not the right size or shape to be grippable with of any of my chuck jaws, and that's pretty often, I do what Mike suggested and reverse the bowl one more time and finish the foot as he said.
One day when I grow up I'll get a vacuum setup just like the big boys (& girls) have; I used one for the first time a few weeks ago and they are pretty slick.