Understanding (and fixing) non-manifold geometry

I’m trying to understand Blender constructs and manifold vs non-manifold geometry.

I do a lot of modeling for 3D printing, so really need to get this right.

I’ve looked at a number of tutorials on YouTube, and Googled the subject extensively, but still cannot find anyone/anywhere that explains the basics. I have tried all sorts of things, but I’m still confused.

Let me start with an example:

I’ve created a cube manually.

1)Set Snap-to to "edge"
2)Turn on Snap
3)Add –> Mesh –> Plane
4)Copy plane –> rotate 90 degrees on the x-axis
5)Move new plane and snap to edge of 1st plane.
6)Repeat (similar) steps 4-5 for remaining 4 sides of the cube
7)Join all into one object
8)In edit mode, select all
9)Merge vertices (by distance) and confirm only 8 vertices now exist
10)Using 3D Print addon, do "Check All"

This shows 20 non-manifold edges. If I use the addon’s "Clean Up" –> "Make Manifold" option, it removes three of the six faces and still shows eight non-manifold edges.

I simply don’t get it. Can ANYONE help me with my understanding or point me to a place where I can get it?

Many, many thanks in advance!