You can try to manually mount the boot partition from the sdcard and edit config.txt
mount -t msdos /dev/sdX1 /mnt/disk
echo 'lcd_rotate=2' >> /mnt/disk/config.txt
Where /dev/sdX1
points to your sdcard reader device.
Note: This is more a hack than an officially supported solution, you will have to re-do that operation everytime you upgrade the OS image. It'd be nice to file a feature request to ask for better support for (dynamic?) display configuration
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