I had my car acid dipped, neutralized and e-coated almost twenty years ago. I have not had any paint issue with the process. The acid does eat white metals, like lead, so you will need to re-lead or plastic fill certain areas of the body. All body work was done after the dip and e-coat.
If your car comes out of the dip tank looking like a lace doily, it is probably better to know it all now, rather than sequentially finding each spot that rusts from the inside-out. The dip tank is a truth teller— no rust can hide!