Genetic modification often produces altered proteins. These protein signatures do not match human T-cell allowlists, causing immune response.

Even if the modification is a simple addition between adjacent start and stop codons, that kind of modification could alter meta encodings that control other aspects of cell regulation, including (potentially) gene expression -- which would cause proteins that are coded for but that normally aren't present to become present in crops. Even one newly expressed protein (that is normally not ever expressed) could trigger immune response.