Custom Tune vs Box Programmers
With a custom tune the vehicle is able to be data logged via the primary sensors used to tell the ECM how to control the vehicle and tell it how to run.
The engine side of custom tuning:
A few examples of the sensors include the MAF, air intake temp, o2 sensors for the long term fuel trims, short term fuel trims and knock sensors. With all the combined data logging of the sensors used to run the vehicle the tuner can make adjustments to make maximum horsepower and torque with maximum timing with fuel octane used on a daily basis, achieve better fuel economy and make sure the air to fuel ratio "AFR" is correct. This will keep the vehicle from running to lean of fuel or adding too much fuel and becoming to rich either of which could result in hurting the engine or worse. The tuner can also make adjustments to the top speed limiter, rev limiter, idle rpm in P/N and drive with AC on/off, electric fan cut on/cut off temps.
The transmission side of custom tuning:
With a custom tune the tuner can make adjustments to transmission shift pressure and shift firmness, shift speed "MPH" under part throttle, full throttle, full throttle shift via rpm in both drive and tow/haul mode. Changes can be made to the torque converter clutch "TCC" lock up and unlock. Torque management is also adjusted per driver demands/wants for faster shifts between gear changes for both drive and tow/haul mode.
Here at Mag's Tuning we do real world street tuning so that the vehicle is tuned in the everyday conditions that the vehicle is driven in. Unlike dyno tuning that usually only results in wide open throttle "WOT" tuning unless the tuner is using a load bearing dyno to "simulate" a load on the vehicle i.e wind resistance, change in road conditions etc etc. the vehicle may not change much for daily driving and could actually get worse.
*All vehicles tuned by us immediately has the stock tune file pulled, a copy made of it, and saved to a separate hard drive. As well the computer used to tune the vehicle will contain the same information so that at anytime there are two stock tune files if the owner at any point decides to return the vehicle back to stock. We only use the 3rd copy of the stock tune to make adjustments.*
While most box programmers do add and offer a slight performance improvement over stock, they were built in a controlled environment under ideal conditions in a temperature controlled dyno room allowing for the best air intake temps on one specific vehicle. These tunes are then dialed down for allowing them to tune other vehicles of the same engines and transmissions extremely safely to keeping the engine from causing knock retard "pinging" which will result in damage and the transmission from tearing itself apart. Box programmers are a generic tune that isn't designed for your specific vehicle they can't truly unleash what your vehicle is mechanically capable of making. They have to dial them down because they have no way of knowing exactly how much timing your specific vehicle is safely allowed to take for maximum performance. Transmission tunes in box programmers have limited setting options that are usually percentage only adjustable settings. In conclusion box programmers are very limited as to what they can do for your specific vehicle and when compared to custom tuning it's like comparing apples to oranges, while both are edible they offer two completely textures and flavors.