Actually I don’t know and never really found an answer to that.
I normally tend to change the config.txt before(!) the first boot and include everything there.
Be advised that after the first boot, the config.txt will be “checkum controlled” by the supervisor, meaning if you change something by hand (e.g. when the RPi is off and you reboot), the supervisor will find that change, replace the config.txt with the last known value from its sqlite database and trigger a reboot, undoing your change. You have to manipulate the entry directly in the sqlite database to make it happen, at least that was the case when I did it the last time… But maybe some of the balena Wizards got a more obvious way of doing that or at least a less cumbersome