Smidlee, the comparison doesn't work. They are talking about highly conserved and identical sequences of RNA. The reason why they say they're primordial is because they are quite literally identical in all walks of life.
When you look at ATP Synthases, the DNA and amino acid sequences vary wildly and the mechanisms of action vary wildly from organism to organism. Unsuprisingly, the more complex the life form (and hence a larger energy output required), the more complex the ATP Synthase enzyme. In fact, it is just further evidence of evolution in action, as they have similar functions but have evolved to meet the energy needs of the host organism.
What many of these papers are talking about is a world prior to ATP Synthase as we know it. They're talking about life in a much simpler form than any life found today. No DNA, proteins or enzymes. A world consisting of RNA and ribozymes, catalysing their own synthesis, and where these molecules are originally formed by catalysis via inorganic sources such as metals and clays (see first reference).
You obviously read science, but don't actually grasp the concepts and then twist things to suit your point of view. Taking your car analogy, the early living organisms wouldn't be a car with no petrol, but would be like the first ever car (as in steam powered) and current life would be like the modern day, high performance, gasoline powered cars... like a Bugatti Veyron.
Conclusion: Science is constantly working to improve our knowledge of life using facts and evidence (and not the manipulation of quotes and the bizzare logic you seem to present) rather than placing blind faith in a god whose existence is unknown.