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Philosophy is "eternally supreme" over empiricism? Hardly.
This is an absolute truth, so I suggest you think about how you are wrong on this one.
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Philosophy is merely a weak substitute for empiricism in regions where we don't yet have tools to access information with empiricism. Luckily, philosophy of the gaps shrinks as time marches on. Just as Greek debates about atomism have passed from philosophy to science when we developed the empirical tools to answer the question for real, so too will current philosophical debates pass into the realm of science eventually.
Your example about atomism is a philosophical question that is in the realm of empiricism - how far can we divide matter? Is matter discrete? The questions are exactly what empiricism is designed to answer - what are the rules governing the physical world?
But you are thinking far too narrowly. Your brain has clearly been rotted by empiricism. Below is a tiny fraction of the important questions where philosophy will always - regardless of what we know - be more important than scientific results:
How should humans live?
Should there even be a "should" that we apply to everyone?
Is it right to maximise happiness, or is human suffering a important part of who we are?
What is the value of a life?
According to what principles should we organize our social and legal institutions?
It is right, or desirable, to err on the side of freedom, or safety and control?
Is slavery tolerable, or even good, in the grand scheme of things?
Is the individual more important than the whole?
I defy you to tell me any way in which these incredibly important questions have been answered by science - or even could be.