There is a general confusion of what header side is left and right. For example, if we take pin gpio_23.
In the pcf files it's listed as 'left'
# Normal GPIO pins, left side
set_io -nowarn gpio_23 23
In the schematic it's on the right header symbol
In the Kicad 3D rendering its on the right header.

Please fix it to have consistent and intuitive orientation. This can be done with spinning a new PCB by
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In the schematic swap the positions of the two header symbols.
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In the headers footprint, rotate the 3D model of the pins to be on the other side of the PCB.
This will make everything consistent for this 'canonical' orientation (view from top):
