Here's a cone view.
Everything from large trees to atoms are viewed by our eyes in the cone view (just my perceptions...). This is a very interesting concept. It's like shooting an electron (into or out) of an element, that changes an physical & chemical properties of the atom, compound and substance etc..
Think about a pencil, and what it's made of.
This may be quite far from a deep chemistry expertise. So take this as a simple representation to accommodate the diagrams that you began with and looking from a different perspective. We aren't trying to fit a facts/theory into our understanding and visualisation but other way around.
An important distinction is the clarity of molecule, compound and mixture.
Molecules are constructed of atoms of same species. A compound is formed by atoms of different species. Compounds are of 2 different types mainly,
Each of this bonds, origin goes back to a single atom and involvement of its orbitals energy and electrons.
For an example,
The water that we drink is a molecule and also a compound, made of two H atoms and oxygen atom covalently bonding. Isn't it odd to read in your paper or an article, "the water compound..." or wouldn't it feel fit to read as "a water molecule...".
The salt we add to balance flavour is a compound, made of one sodium atom (+charged ion) and chloride atom (-charged ion) ionically bonding.
The air we breath is a mixture of various molecules : $H_2O, H_2, O_2, N_2, CO_2$ etc (not atoms).
Put it this way, all compounds could be molecules, but (not) vice
Here's the top view (transverse plane from the very top) of the cone.
In physical sciences the matter is classified in pyramids like the following. Reference is in the image itself.
There are more advanced and slightly different version of discussions on the same topic here on pubchemblog : "difference between xyz..."..
The starting cone isn't pretty as your images. But I will make them more user-friendly and eye-candy if you can comment. This almost feels like a drawing session now, apart from the conceptual outlook. I am happy to read more about intermetallic and coordinate bonding as well to address that in the answer. It is not something I come across on daily basis as I am not in electronics or soldering/alloy analytical chemistry. Apart from the cone, other picture references are taken from here.