Another option, albeit a more pricey one, is to go with a standalone ECU tuning setup. A standalone ECU replaces the factory ECU with one that can control a wider set of parameters. The name aptly describes what it does, it stands alone from the factory ECU, controlling everything the factory ECU does and more. Standalone systems allow you greater levels of customization and control when it comes to tuning your vehicle, essentially giving you the power to tune your car from scratch, dialing in your engine's parameters to your precise liking.
So, if a transmission has a stand alone ECU, it will not shift based off of the stock ECU's input. The transmission would have its own computer system. This can be beneficial in instances where the stock ECU can not supply the necessary computations for the transmission. Additionally, stand alone units can handle more power and precision when it comes to tuning and aftermarket applications. They are especially useful in not stock applications, where a stock ECU has a transmission attached to it from a different model (IE: Coyote and 4r70w).
In all honesty, unless you have a HIGHLY modified Mustang (talking body panels that have been replaced with lighter fiberglass or other materials), tubed chassis, aftermarket crate motor, boost, and everything in between) that is strictly competition use, then standalone tuning doesn't make sense from a practicality or financial standpoint.