Did more testing. This time I really found some stuff out. If you replace the sr3_city.lua. It will disable the controls.
If you replace all the the files in the cache folder, tons of bad things will happen such as music stopping, no hud, pausing the game will freeze the game too.
I did however did another test to where I used all the vanilla files in the cache folder with the exception of the rigs file and the misc tables(your misc tables) and it looked so far so good there.
EDIT: I think I forgot to update the ASM. Might need to reinstall the beta again but I can verify that the sr3_city.lua file being replaced will disable the controls for the sandbox.