The Atlantis\launch.lua script doesn't work correctly with the 2016 stock Atlantis. It has been replaced by the AscentAP MFD mode. The reason is that the Lua script (incorrectly) uses RCS for attitude control during ascent, while AscentAP uses the SRB and SSME gimbal capability introduced to the 2016 Atlantis.
There was a significant rewrite of the Atlantis code for the 2016 version (for example, the launch stack is now composed of individual docked vessels, instead of a single vessel containing the entire assembly). The Lua launch script was never updated or tested to work with the new version.
If you are interested in updating the Lua version of the launch autopilot, one prerequisite is exposing the Atlantis gimbal control functions to Lua. An example for how to add vessel-specific Lua functions is given in the Deltaglider code. Have a look at Orbitersdk\samples\DeltaGlider\DGLua.cpp to get the general idea. You could then start by re-implementing Orbitersdk\samples\Atlantis\Atlantis\AscentAP.cpp in Lua. Once you get the same behaviour, you have a platform to experiment further.
Vehicle I tested upon: OV-104
If you are not talking about the stock Atlantis, then all bets are off. You won't have the AscentAP MFD mode, and the Lua script may or may not work. Default assumption should be that it doesn't, unless the addon developer explicitly checked it. In any case, an RCS-based ascent AP is a fudge and should only be used as a last resort.
