Assuming that azo food dyes containing sulfite side chains can be acetylated just by coming into contact with yeast-released acetaldehyde in the gut, then why would that trigger an immune system response?
Drug delivery experiments have shown that acetylation increases the bioavailability of orally ingested molecular configurations [*]. This implies that a much higher concentration of acetylated food dye molecules could potentially migrate into the bloodstream than if they remained in their native (unmodified) form. Once in the bloodstream of sensitized individuals, the immune system would respond to these invasive chemicals as allergens. And even if the response is not a classic IgE mediated one, the potential pseudo-allergens are being delivered to cells throughout the body as if the food dye had been injected rather than ingested. In the yeast/acetaldehyde model the degree of acetylation of ingested food dyes would depend upon the yeast colonization locale and level in any given individual and upon other dietary constituents that favored budding yeast metabolism of carbohydrates to form acetaldehyde.
[*] Ogiso T et al., "Enhancement of the oral bioavailability of phenytoin by N-acetylation and absorptive charcteristics.", Biol Pharm Bull. 1998 Oct;21(10):1084-9. http://www.ncbi.nlm.nih.gov/pubmed/9821815