You can try to manually install the boot partition from the SD card 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 SD card reader.
Note. This is more of a hack than an officially supported solution, you will have to repeat this operation every time you update the OS image. It would be nice to submit a request to ask for better configuration support (dynamic?)
proppy
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