Intersect Face-3D-Print\Mesh Analysis issues

Blender 2.90.1

I am trying to maintain clean geometry in models while building them, and have started to notice some discrepancies between the 3D-Print add on and Mesh Analysis callouts.

I have attached the basic model file. In adding a Boolean modifier (DIFFERENCE) to the BASE object for each cube (separately at first) and checking both tools (3D-Print\Mesh Analysis) individually, I started seeing “Intersect face” issues under “3D-Print” that are not being reported under “Mesh Analysis”.

Is it the Boolean modifier creating the issue? Is it the way I created and positioned the OBJECTS? Sequence of Boolean operations? Is “Mesh Analysis” seeing something different than “3D-Print”?
From my perspective, the Booleans being made are not being applied to a complex OBJECT. Does the 3D cursor need to be at the difference OBJECT creation point? Booleans have been applied to the BASE prior to checking. Face orientations are correct after applying. I also see more issues being called out in 3D print when “Cube 003” is used as the Boolean. Even starting with clean Blender files I can reproduce it.

What “EXACTLY” is an “Intersect-Face”? Is it a face that has a Boolean modifier applied to it? Is it a Boolean face that overshoots a perpendicular plane, thus the Intersect callout? By applying the Booleans separately and then in different combinations, I get different callouts.

In searching and watching videos, I can find items regarding it, but they all seem to “DANCE” around what it is, how to avoid or resolve it. Many articles say that by deleting the face and then creating the face fixes it, but that is not my experience. I have read that some 3D printer software can deal with them, and I saw an article saying that using “MATCAP” can create the issue.

Intersect_Face.blend (762.7 KB)