Theming through Optimizing Physical Directory Structure

I have a question specifically related to “theming” a website (siloing, etc), specifically through “physical/directory siloing”.

Given the following conceptual website theme and category division, how would you set up your directory? (If anyone has a reference to an article/video/blog with discussion over the various options, please point it out…)

Now, look at the three “category” or “silo landing pages” at the top. I would probably create this, physically, like this:
Option 1

Option 2
BUT - many sites do it THIS way.