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The Versatile Channeler Feat allows a Neutral cleric of a Neutral god to channel both kinds of energy, with the secondary one running as if your cleric level was 2 levels lower.
But, how this interact with Variant Channeling? According to UM, "A variant channeling either modifies positive energy when used to heal or negative energy when used to harm".
The question is: a cleric could use the "standard" channel positive energy and a variant of channel negative energy? For exemple, could a Cleric of Abadar channel positive energy in the standard mode and the Rulership variant for channeling negative energy?
I would say that you would use the variant for both Positive and Negative. If you select Rulership as your variant, when you heal you grant the Diplomacy and Charm spell bonus and when you harm targets gain dazed affect.
The section clearly states: "Feats and abilities that modify or present alternative uses for channeled energy (such as Command Undead and Turn Undead) work normally with these variant channeling abilities."
So Versatile Channeler applies normally. When you make the Character (or first gain channeling) you decide to take Variant Channeling, then at a later level, you gain versatile channel, but you keep Variant Channeling.