well flux core, like solder, is filled with an acid solution if u remember. so it helps clean what ur welding but any element can get into and contaminate the weld, including the acid
by having a welder that has a bottle, usually 75%CO2/25%Argon or 100% Argon ( for aluminum and i think copper), it allows or a much cleaner and better weld. the gas makes a shield that protects the weld from the elements that would normally contaminate the weld.