There is no provision in any Honda model for "speedometer calibration".
Some Honda models with indirect TPMS and that offer different wheel sizes such as the Accord have a setting that can be change using the i-HDS for wheel size, but this is to change the peak resonance frequency which the indirect TPMS uses to detect a condition where all four tires are equally low and does not apply to the Passport.
The "Yellow Box" and similar devices can cause all sorts of unpredictable problems with newer vehicles that measure vehicle speed using not only the output shaft speed sensor in the transmission, but also each of the four wheel speed sensors. When the OSS sensor says the vehicle is traveling 70 MPH and the wheel speed sensors say the vehicle is traveling 65 or 75 MPH, certain modules may set DTC's and certain function may not work or not work as expected (such as stability control and automatic emergency braking).