I'll take at stab clarifying things. I haven't taken the class and I'm no expert, so just take things with a grain of salt until someone more experienced can answer!
For the soil example- yes soil values vary, so you just pick the local value that works for your piece or for the environment design.
For your first illustration example, the character is in the extreme foreground and looks mostly back-lit so he will be darker. The background has atmospheric perspective- since we are seeing the background area through layers of atmosphere the dark values will be lighter. The character may have less overall value contrast because he's mostly in shadow and his character design choices just have less local value contrast between his clothes, skin, and hair.
The second illustration looks like a different lighting situation. Your first one looks like either a foggy day, or late day scene. This pirate one looks very sunny and bright- more in direct sunlight- so lighter values are going to be lighter. Light will also bounce around all the surfaces and potentially make some shadows lighter. This piece is also utilizing line work to help with contrast and is not just relying on light and shadow. The artist looks like they chose the value of the wood of the ship, so he/she could contrast the characters off of it. Just like the soil example, wood can have different local values and you can choose the one that will give you the best pay off. It also looks like the artist is using some atmosphere or light bleed onto the ship in the lower left side to lower the contrast of the shadow on the ship and keep the focus on the characters.
The third example- first I think it looks more graphic and you can really play around with values without worrying about realism of light and shadow with graphic styles. But for this one atmospheric perspective can be at work on the waves. The ship is also mostly running perpendicular with the ground plane and could be back lit, while the ocean is running more parrallel with the ground plane and light could be washing over it's surface more.
If you DM me your email, I'll send the files to you in a non psd format.