"Just for some perspective, scientists have the nature of matter itself absolutely figured out now , right?"
Foul ball!!! You have to say in the lines!
It seems even Nobel Laureates are having a hard time figuring such mystical quantum revelations about things like particles revolving both clockwise and counter-clockwise at the same time. As they say concerning QM, the more we understand about this, the sillier it gets. To me, that just leaves the door open to things such as a possible force outside of what can be known as having started all of this. QM is so cool!
And I'm someone who agrees with some of the logic behind evolution. But why throw the baby out with the bathwater? Just because something isn't endorsed via scientific method doesn't mean it can't be happening. All kinds of inductions can be made from QM.
And remember, some of Einsteins work was theorized via thought experiments. And also some of science thought to be rock solid (oops, guess there's no such thing, just wavicles) gets absolutley turned on its head when thought to be fact through the years.