Here is an example to show what I mean
Ungrouped Object (Red background for illustrative purposes)

It is layers like.... Solid black-filled bat background, Smaller white-filled bat on top, Black highlights
Selecting all the items gives me this:

That is the desired result. This is great for one image, but I have thousands to process, and I'm not sure this will work for all of them.
So my questions are 1) What if I had more objects and multiple white sections? Will this exclusion selection always give me the desired result? and 2) Is there a better way to do this? 3) How can I script it with inkscape? Seems like there is a limit of what can be done via command line.