The allowAutoSmelt and allowRepair boolean config for random leveling modifier is not turning off when it is "false" in the config file. I am using Version 2.1.2. I get these modifiers on my sword and bow, but not anything else.

Disable completelyRandomBonuses.

It is disabled, It respects all other config settings, but autosmelt and repair are still applied at random.

It is impossible to get a modifier that is disabled or not-useful with useful bonuses enabled. Your configs are probably incorrect.