Most GMO is trans species. For example,Golden rice is two genes that collectively synthesis beta carotene, the metabolic precursor to Vitamin A. Psy is from the daffodil. Crtl is from a soil bacterium.
It is estimated that annually, about 500,00 children under age 5 going irreversibly blind from vitamin A deficiency, VAD, and that VAD contributes to up to 2 million deaths. There are about 190 million children with VAD, most in Asia. And this GMO rice is available free thanks to Syngentia and the inventors generosity concerning patent 7838749 and its sequelae.
The example shows how narrowly specific GMO actually is. It does not ‘scamble up’ the general metabolism as you seem to fear. As Matt Ridley pointed out in the WSJ recently, the older way (screening radiation induced random mutations for useful properties) is much more likely to result in unintended consequences.