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Just to focus on a few points:
1. I think it's a real stretch to say that transgenics are based on a "one gene, one protein" model that has subsequently been found to be completely false. While we are still discovering complexities about what are genes, and how they are regulated, alternative splicing, post translational modifications like phosphorylation and glycosylation, and protein degradation which are major drivers of the complexity which gets you more proteins than genes, have been know about for decades. These factors can contribute to your transgene not performing as expected, but that doesn't mean that the underlying rationale was mistaken. This is why you create multiple transgenic events and select the ones that are doing what you want.
It is possible that inserting a transgene could have effects on other components of the organism that weren't anticipated and may or may not be detected by current methods. Of course this is true to some degree of any genetic modification, be it a 'naturally' occurring mutation that a breeder spots and uses in their program, or the results of a widely diverse cross the breeder makes.
Which brings me to:
2. The fact that the genetic modification goes in randomly and induces a lot of genome shock is not really a big cause of concern. There are lots of places where an insertion will have no effect, and lots of places where it will have an effect. Thats why you do multiple events and select for the ones that work (and don't disrupt other genes). Most of the other changes that are induced by the insertion event are cleaned up by back crossing to the parent. Again, this is very similar to conventional plant breeding.
While I certainly think that much more food safety testing could be done, I haven't seen convincing evidence that makes me worry about eating transgenics. Most of the studies cited by Lotter which claim to have shown severely negative consequences of transgenes really are poorly done.
note: given my occupation and aquaintances, I'm sure some would consider me to have conflicts of interest.