The recognition of nucleic acids is a pretty old and evolutionarily conserved arm of the immune system, regulated by receptors called 'Toll Like Receptors' (named because the German scientist who discovered them in the lab called them 'toll', meaning 'cool'.). Their whole role is to recognize 'coatings' that are used by bacteria, or nucleic acids (single, or double-stranded RNA) used by viruses or bacteria.
While the nanoparticle coating could potentially diminish 'free' RNA from floating around, I'm not sure that's the mechanism here as TLR receptors cycle into the intracellular space, basically to monitor for the presence of infection. This pathway gets abnormal in people with autoimmune disease, for instance, where the body starts making an immune response to normal cellular RNA and DNA (like in lupus). Basically, there immune system evolved to deal with the threat of nucleic acids floating around that don't belong there.
I think what's being seen with those with severe allergic hypersensitivity will see it with either RNA vaccine, or at least thats my guess. Again, these are people who have such hypersensitivity they have to travel around with EpiPens, so it's not just people like me that sneeze in contact with anything flowering or furry.