Well... ahem... erh...
Actually it is called custom_missions.tmc, while the generator calls it custom_mission.tmc. Mind the missing "s".
Yes I noted that 😀 I did change the name to custom_missions.tmc but I did not still find the mission in Aerofly FS4. Should it show up under Challenges?
I created a simple flightplan with departure from EFTU airport, with a single waypoint (just a latitude, longitude location). Does it need to have a destination airport?