I've only used the muriatic acid on clear zinc, since RoHS started the process of making yellow zinc extinct. My main personal concern isn't zinc contamination of the weld, it's health. The zinc oxide gas generated is not good to breath, and that's of particular concern to me.
Possibly TMI: My father and his brother both died horrible deaths from ideopathic pulmonary fibrosis, which causes lung tissue to degrade over time and stop pulling oxygen from the air into the blood. Those with it gradually suffocate to death. Ideopathic means they don't know what causes it. Because two siblings died from it, they were both in a long-term study at the University of Denver, as are myself and my two brothers, as the second generation (fortunately, none of us has any symptoms, yet.) The researchers there are working through a theory that a particular gene sequence is required, but something environmental triggers it. They are close to identifying the gene sequence, but the environmental triggers are still a mystery. For that reason, I'm very careful with keeping odd things out of my lungs. I saw him tortured trying to breath the last six months of his life, and I'm doing everything I can to die some other way...
It's funny because the fumes from muriatic acid aren't exactly healthy, either. But at least with that, I can do is outside, and I just set the part in the acid and walk away for a few minutes.