The Pickup and Switch settings can be accessed through cog as sets of flags. The SetAuto verbs do not act like normal verbs that set flags. Most flag verbs only add flags, but the SetAuto verbs set the total flags.
For example, if you use SetAutoReload(player, 0x8), the 4th Weapon Pickup1 checkbox will be checked, and the other three will be unchecked no matter what they were before.
Because the SetAuto verbs don't work correctly, there is no known way to set the Reload Weapon options. There's a seperate column of checkboxes for the SP and MP options. The option verbs will use the appropriate column depending whether the game is SP or MP.
Unless the player opens up the gameplay options and saves them, the settings changed by the SetAuto verbs will not be saved when the game is exited.