Find here an overview about handling of game resolution for a specific parameter settings.
You want to play vertical games on horizontal screen. Then set auto_turn_screen to No and game_res_mode to no and fixed resolution from custom_resolution_table.txt for vertical default resolution will be taken.
You have a cab with rotating screen. Your game menu is horizontal, but games shall be displayed vertical. Then choose auto_turn_screen yes and enjoy native displayed resolutions.
You want rather go with hand picked resolutions instead of computed ones, Then set game_res_mode to yes.
Just make up your mind about your cab and adapt the parameter settings.