It calibrates the speedo based on the tire size and gears YOU programmed into it. Therefore, if you have different gears or a different tire size than what you put in there, your speedometer will be off.
Since you have programmed the computer for 3.88 gears, your speedometer now assumes that you have 3.88 gears in the differentials. Since you don't have 3.88s gears, your speedometer will not match your actual speed. (it'll be off by about 4%)