You’re overthinking it, take it at face value and it really is simple.
If you set the GPIO14 sensor to 09 Switch1 in the web ui, the state of the switch is triggered when there is a change in the state between GND and GPIO14 on the board, it doesn’t matter whether it is low to high or high to low, if the switch is on it will go off, if it’s off it will go on, in your terms the way up the switch is is irrelevant. The Sonoff broadcasts it’s state to MQTT so HA reflects that in the front end. This is why you can use a traditional switch connected to GPIO14 and GND on the Sonoff to toggle it rather than kill the power to the whole thing. You do that to your other light as well so you have to independent switches operating the same.
The magic happens when you then set up the automation in HA as I have explained before, you use the trigger of the state of one light changing to toggle the other and vice versa, simple as they come.
Then you’ll have what appears to be a normal two way circuit, using three way switches if you want to use the daft US naming convention, which can be controlled by either of the physical switches or any number of remote ways via HA and everything will stay perfectly in sync.