As far as I understand, the idea behind synthesized fuel is to bind CO2 to create the fuel, which theoretically should make it net neutral, if one ignores power consumption and chemical usage, as well as the CO2 probably not being sourced from the atmosphere.
In other words, the technology should be sound enough, but it will most likely not be used for good, as per my first post.
Then we come to the other issues I mentioned. The fuel should theoretically be CO2 neutral, but the plane does not fly where the factory is located. It flies some ~10km above surface, which means that we are pumping CO2 into the middle layers of the troposphere, which probably is bad idea.
Edit: i realize that I formulated myself in a rather unlucky way in the first comment, whelp.