I have no 7" display here, but there is a blog post (https://www.balena.io/blog/running-a-desktop-manager-with-balena/) about running a desktop manager on balena. It has a section about rotating the screen as well. It depends on how your screen is connected:
HDMI: To configure the Raspberry Pi to use the HDMI connector, click on Device Configuration and at the bottom where it says CUSTOM CONFIGURATION VARIABLES, add new custom variables:
CD DSI Display Connector: In case your display is attached to the DSI connector, you can add the custom variable
BALENA_HOST_CONFIG_lcd_rotate with a value from 0 to 3 which corresponds to 0, 90, 180 and 270 degrees.
I hope this is the answer you were looking for.