The thing with doing it through just programming is that the only way it can be done is via jacking up the line pressure. This can definitely cause longevity issues or stress failures.
Think of it like your circulatory system. If you have restricted passageways, this makes your heart work harder which raises your blood pressure. Raised blood pressure causes several problems. First of all, as mentioned, your heart is working harder and that is always bad when it's against a high line pressure and not from normal usage. Then, you have the added pressure in front of the restrictions and that can cause something to burst. All very bad.
Would your doctor prescribe a medication for you that raises your blood pressure so you can get better performance? I don't think so. I think he might suggest excersize and a diet to improve the flow of your circulatory system.
Regardless of how silly that sounds, it's the same for your truck. If you give it something that raises it's line pressure the pump is always working harder while the restrictions stay the same size. This will wear out the pump and increase the chance that any weak passage wall or seal might let go.
With a modified valve body the shift improvements are from modifications that allow increased flow at the same line pressures. This results in much quicker shifts that help the transmission live a longer life without the added pressure that will definitely also shorten it's life.
The reason the factory can't do it, or trust me they would, is because most people like to feel as little of the shift as possible. And, almost all of the modifications that are made to the valve body kits mentioned already were actually 'prescribed' by one of the Ford transmission design team engineers.
Just something to think about.
Darrin