FCAW should be cleaned before being topcoated. The "flux" is the same material as the coatings on SMAW electrodes. It is fairly inert material and degrades mostly into ash and CO2 during the welding process. Most flux is cellulose (dead trees, paper) with stabilizers. Structural steel procedures call for the aggressive removal of welding slag prior to treatment or top coating. Welds are wire brushed or media blasted (which peens and evenly distributes stress). I have seen a lot of welds in my day and I don't remember seeing one that looked like the slag promoted rust in it's self. The slag and resulting voids can help in retaining water and mineral salts that promote rust. There are a lot of naked welds in the world. Slag is also fragile and subject to cracking (or popping off) due to flex or impact which can let water or other nasty stuff under your finish. If you want it to last it should be cleaned and sealed. FCAW or dual shield is spec'd in most structural steel not GMAW(MIG). GMAW welds have no impact value (Charpy). Second spec'd is good old SMAW(stick).

Jim

Good luck with your project!