the command point option does nothing but make the command points temporarily high so you can keep building ships. turn it off and go to next turn and your CP will be back to normal
the trainer is working as it should. the problem with negative numbers is basically that the high values being used sometimes are written as signed numbers (i.e. negative). save your game, close the game completely and then restart the game fresh from steam and then LOAD your savegame and then turn the options back on or try money again. i have no other suggestions.
I have tried to modify some files and it just doesn't do anything.
I tried to change the production price of the Charging Hub, since 250industry at the start is insanely high....but nothing works....so i gave up.