Currently the auto lights do a pretty decent job at toggling the different lights on and off when needed except for in a few cases:
Entering/being on the runway
When on an active runway, the strobe and landing lights must be on. In game, those lights only turn on when you are above a certain threshold of throttle percentage. You could implement a contact box and copy and paste it onto each runway such that once a plane is in it/touches it, its landing and strobe lights automatically turns to on. (Not sure if it's a convenient bug but this actually happens somewhat at Enoksen)
Engines off in the air
Naturally, when the engines are on off, all off the lights turn off. An aerial plane without fuel should still remain visible and I suggest that they lights are coded to remain on above a certain altitude. This could be implemented in a similar way to how flight minutes are only awarded (without the aerial airspeed part).
Landing/slowing down
When landing, as soon as you turn on the reverse thrust, the landing and strobe lights turn off. This is arguably the worst part of the flight for the auto lights. My suggestion for this is for the lights to turn off only when under a certain speed when on the ground. This one is particularly for maybe emergency landing in a field or so as the first suggestion should cover for designated airports.
