The pull up on data0 and command lines are used for "in case".
In case, there is some hardware layout issue for example need to debug hardware.
add the external pull up can make the ware form better in case layout has issue.
When you debug hardware, you can use the 1 bit mode for emmc. that is why you can see the pull up only on data0.
also suggest you can add one 0 ohm series resistor in the clk "in case" need to debug the hardware for timing issue, which also may be caused by layout sometime. You can adjust that series resistor.
The pad/pin settings are independent as show below picture. no related to GPIO. related to IOMUX.
The GPIO, ADC, SAI are equal.(In blue of the picture). they only take of care of logic "0" or "1"
The pads/pins(silicon ) is in red.

