I’m late to this party and tried to skim the two related threads. Please forgive if I miss pertinent posts in my remarks.
Before Luther posted his 95 Theses in October (1517), he posted 97 Theses in September against Scholastic theology. In the 97 Theses you find Luther struggling with the notion that the scholastic ethos, what has been called here A-T philosophy, tends to take on a life of its own. What I mean by this, and what Luther argued in the 16th century, is that the inner workings of (Neo)Scholasticism become more valuable, more true than the world itself. The system is worth saving at all cost regardless of what “data” is marshaled against it; the “plain facts” – whether atomistic or holistic – are subservient to the metaphysical Scholastic system. Luther saw this played out most fully with his 95 Theses regarding sin, grace, and indulgences. However, a scientific analogue was tested at Luther’s Wittenberg with Copernican astronomy as well.
The Lutheran approach, at least in my humble opinion, will be to stay neutral on much of metaphysics. What this means at a practical level is what many of you have been saying already. It is unclear how AT actually influences/helps the scientist in the lab. The difference, however, is in what AT inclined thinkers say regarding the value of AT in explanation or understanding the larger world. AT style thinking is keen to see the entire universe in coherence. Lutheran metaphysics, if I may use the term, will always see a disconnect with any coherent system of thought and the way the world appears. This is more apparent in science as our knowledge can literately change before our eyes. It is less easy to see in metaphysics as those theories rarely go the way of the dodo, but get repackaged in new language.
This disconnect between believing that the world is more than it appears, yet limited to the world as it is given is the paradox or tension in Lutheran thought. We are free to build metaphysical systems, even AT style systems, but will always be leery of the potential for idolization. The system is fallible and must be able to fall, forgetting that we’ve sold our birthright. In that vein, what would make the AT system false? Or, another way, what state of affairs would cause an analytical Thomist to give up their system in chemistry or otherwise?
The big players in the Christian philosophical world are variations of AT and variations of Plantinga’s Reformed thought (which draws heavily on Aquinas!). The view you seem to be in alignment with would be some sort of nominalism/skepticism in your epistemological stance that colors your metaphysical positions. This is where I often find myself as well. It isn’t quite as sexy as AT or RE as it doesn’t tend to tie up all the loose strings in a nice neat package. But then neither does the world seem to be a perfectly packed ball of string! I guess I am much more comfortable with uncertainty and remaining agnostic as to properly deciphering primary/secondary substances alongside quadruple causes.