As of Hotfix 2.20, when spawning or moving a VTOL aircraft on a ship via script and assigning it a valid waypoint, the vehicle will refuse to lift off. Furthermore, it also seems that VTOL's (placed, spawned, or moved) on the flight deck slowly begin to tip over slowly until either their wings/blades touch the deck, and only after teamswitching to the pilot will the vehicle right itself back to normal.

Additionally while the VTOL is on deck, if either the pilot's group OR the waypoint's behavior is set to "SAFE" or "CARELESS", the vehicle will immediately shut off its engines and ignore commands like 'engineOn'.

This was encountered the June 26th, the day after Hotfix 2.20 dropped, and affects all VTOLs as per my tests. There were no mods loaded into the game, only the applicable DLC's. The only way around these issues were if the player piloted the VTOL and lifted it off manually, then switched to a different unit.