Re: deep or short chamber??
The chamber will be cut for proper headspacing and is measured with go and no go gauges. I think what you're asking has more to do with the throat (which I guess is technically still part of the chamber). I would decide what bullet weight/weights you want to shoot and then do what Sask_Hunter suggested and have it throated so that as you wear your barrel out you'll still be able to seat your bullets out close to the rifling.
When in doubt, you could always just have the rifle chambered for a standard throat.