My point with Newtonian physics is that at the time, it was The Physics. According to observation capable at the time, it seemed to make sense, with a few little oddities.
To them, they thought they had a small hole in current physics. Does that sound like your "small hole" in current physics today?
You believe we are knowledgeable, for we posses knowledge our ancestors do not. You believe we are right, for our observations tell us so. Yet how will we observe the universe 1000 years from now? 100? What tools will we have?
Place yourself 1000 years hence. Our ancestors will look back, and see our current physics as we view Romans babbling on about The Elements and aethers. Yes, to our descendants, our science is absurdly simple, filled with holes, broken, the list goes on.
We are not even remotely sure if space/time is consistent outside of our local region of space!
Back to your Newtonian statement, what if all of our current physics was thus? A viewpoint which only worked under certain circumstances. From where I sit, this is the reality.
We work with what we have, but must keep the knowledge of our massive ignorance in play too!