Quantum oracle implementation overhead
As  pointed out by Logan Mayfield, Scott Aaronson's blogpost on the topic completely resolves my question. Oracles is a fundamental tool for rigorous investigation of computational complexity classes, 


  “bring out the latent strengths” of one class over another class.


The root cause of my concerns was that little (as far as I understand - nothing) can be proven unconditionally about quantum speedups in the unrelativized (compiled to physical hardware) world. Of course, this obstacle does not diminish the power of the oracle framework as a major tool enabling progress in quantum computation theory, including the celebrated example of Shor's algorithm.  

Personally, it is a consolation to learn from Scott that 


  This [relativized vs. unrelatized complexity] is an absolutely crucial distinction that trips up just about
  everyone when they’re first learning quantum computing.