Open source work is not a product, it is a gift to the community with no strings attached, and that goes both ways. You don't ask people who give you a gift to then unbox it, set it up, and maintain it for you.
I would argue that the people programming things that are used on starships are not in the field. The people in the field are the specialist who need to be there to monitor and explore. Most of the engineering work of design and development happens on research stations and other places that may not be reflected in Star Trek specifically. It would illogical to send a programmer so far away for work that can be done from anywhere. And that is retaining the concept of programming that is argued by society right now as being in risk. Not to mention that programming is not always by definition writing software at a keyboard.
Coverage on this has been pretty misleading. Posted the full pdf, it refers to other stuff regarding web display advertising. Most news outlets have taken it out of context.
My best guess is that it's simpler for the pilots to focus on the plane because of less interactions with other planes and crowded airspace. The routes are probably simpler compared to domestic fights.