Benevolent Creator God?

[Spongebob]

My favorite argument in favor of God's existence was and always will be the teleological argument, it simply spells out our natural tendency to interpret things teleologically. If by design we mean adaptation of means to end, we can argue that the entire universe is designed and is adapted to life -when I say the entire universe, I really mean it, everything is designed, even things like snowflakes, that opponents of the teleological argument generally present as a counter-example-.

Well, the teleological argument itself is one based on perceived evidence.  IOW, design is inferred based on someone's interpretation of how the universe works.  So this is not an argument to be made without the use of evidence.  Your interpretation of design in the universe is an opinion, but there are other interpretations and other hypotheses.  Now, arguing that a snowflake is "designed" is pretty weak since we know what happens on a molecular level to cause crystalline formation of ice and we can repeat this with variable results by varying the conditions.  Another similar approach is that of intelligent design, which has been demonstrated to be absolutely false from just about everything claiming to be designed, such as eyeballs.  These arguments are weak largely because those making the arguments don't have the imagination to form theories of evolutionary development.

Well, Einstein, in order to formulate SR, still relied on big chunks of classical mechanics, electromagnetism, etc. all of which are based on empirical data. 

No, he didn't.  His fascination with light began as a boy when he saw the light glinting off of the water.  He formed these thought experiments as a way of imagining what was going on.  He didn't use science or math until his ideas were already formed and he knew he needed mathematics to confirm his hypothesis would work so the scientific community would take him seriously.

Well, if it's elusive, then it's meaningless. If we can't correctly assess that some process X is supernatural, then the label supernatural is empty of meaning. A deity may as well intervene through natural processes like evolution and selection, or, to put it differently, only sets out the stage early in the beginning of the universe, and leaves laws of physics take care of it, then interevenes rarely by revealed messages.

I'm sorry if you find the term "supernatural" to be daunting.  I'm not appealing to it; you are.  If you want me or any atheist to understand your argument, then it's up to you to define what you mean by supernatural and you can't just keep appealing to obscure parts of the unknown universe, like quantum mechanics or black holes.

Now you say a deity acts through natural processes.  Well, how are we to tell the difference between a deity's actions and just plain natural processes?  How are we to determine that the laws of the universe are they way they are because of a deity or because that's just how they are?  And how are we to determine when a message is divinely revealed?

But it doesn't matter, the requirement of empirical observation is only valid inside the observable world. If the entity under investigation is not observable or detectable by definition, it's meaningless to require empirical evidence.

Yes, it's only valid because that's the only way it can work.  If you are arguing something not known to exist in the observable universe, you really have only one tool left, and that is logic.