As you already pointed out, the initial values from the manufacturer (EXIF) and the ones in the Pix4Dmapper internal camera database are not identical.
It is a general practice that we refine/calibrate the parameters in order to take into account some systematic errors that would happen when using only the EXIF parameters. Since the EXIF only contains approximate parameters the camera optimization would typically drift toward other parameters (similar for all P4RTK cameras) when using them for processing.
Every camera is different and the parameters can slightly vary and therefore also the parameters in the Pix4Dmapper internal camera database are approximate in the end. Cameras are sensitive to vibration, temperature, etc., and the software will, by default, optimize the internal parameters for each project starting from the initial parameters from the database.
However, we are happy to hear that your customized camera model with the EXIF values worked. As long as you are savvy enough to calibrate your own camera model with the desired values, I don’t see why you should not apply this method.