I've made a project where i use both i2c channels. But the primary dsa/scl has internal 1.5K ohm pullup and some i2c products can't drive that low resistor value. So by using det secondary i2c port (is without internal pullup - must apply extern f.ex. 2 x 4.7K) it now works with both 12c 20x4 LCD display and Pololu imu9-v2 sensor.
I don't know why the board is made different in this matter....