The use-cases of personal flight and mechanical flight are very different, I’d imagine. Flying species will already be severely hampered from using their flight for much, unless Thrive fudges the numbers for the sake of more interesting gameplay (going to post about this) - birds on Earth have had to aggressively reduce their weight due to the metabolic demands of flying, and if you add on the metabolic demands of sapience, well, I think it’s pretty likely the flier might not be able to carry anything at all. Even if they can, a proper plane will be much quicker, and it’ll also have much more durability and carrying capacity. There’d also be limitations on maximum altitude for fleshy fliers due to oxygen, pressure, and temperature.
That being said, according to Randall Munroe, you could theoretically get a plane on Titan into the air with pedal power due to Titan’s low gravity and very dense atmosphere. Under certain circumstances, flight might be effective enough to delay the development of planes - but I don’t think that would require special coding. Ideally, technology development will be fluid enough that the game would take into account this itself (presumably scientific advancements will be modified by all sorts of things, from the amount of motivation to make the advancement to how easy it is to actually do it, and if your species can already fly that would just file under ‘motivation’).