That seems backwards...sounds like saying hot is the same as cold.
Despite what a weapons name implies always look in the description for the exact dmg type it inflicts to better understand what is needed. With a name like protonic polaron odds are it is either going to do antiproton or polaron dmg, but there is that 1% instance of a unique or exotic dmg types.
Proton and Anti-Proton are two difference damage types. So Proton consoles will not increase anti-proton damage. the Proton Consoles are meant to increase the Proton damage proc of the Polaron Protonic Rep weapons and the Experimental Proton Weapon from the Weapon set.