> Farmers have been doing genetic modification to plants and animals for thousands of years
Not with a gene gun, they didn't. Genetic modifications through hybridisation and other traditional methods are protected by cellular mechanisms that are bypassed in GMO.
We'll only see the problems after the corporations make their buck, just like when they gave Thalidomide to pregnant women, blood products with HIV and hepatitis C to haemophiliacs and baby bottles with endocrine disruptors to parents who believed in the magical power of science.
> If they actually are bypassed, the modifications wouldn't give rise to any viable organisms.
Prove it and I bet Nature or Science will publish your proof.
In the mean time, we artificially introduce whole genes in a system made to deal with single nucleotide mutations. It's not like we completely figured out gene overlap, control sequences, that which looks to us like dead code, etc., but we'll fire the gene gun anyway and see what sticks. Meanwhile, the consumers are imagining CRISPR/Cas9-like techniques done by people who understand exactly what and where they are modifying...