If anyone wants to know, I figured out what I wanted to do.
I decided not to contaminate my custom folder with hierarchies for all the custom assets I have, instead, I made a folder in Dropbox for them since they won't take up that much space and I'll install future assets there as well. I'm doing this because I'm also going to use TopHatt's scripts as seen in the video above and use Valve's resident content packer, bspzip instead of Vide or Pakrat. This will allow me to setup independent dev environments where scripts I've configured will create "pure" folders where stock files shipped with the game are placed. So when I'm working on a map, I enable my dev environment and all the stock files are moved out of harms way and another script pulls all the assets I'm using for the map into the "materials", "scripts" or whatever folder so I can see them in Hammer. Then, when I compile, I setup bspzip in the expert compiler to pack content named in a file list I created in Dropbox for a specific map, disable the dev environment so my tf directory goes back to default and I can check to see if everything packed correctly. So after the compile, my tf directory is untouched, and all my content and packing instructions for bspzip is stored in Dropbox and Hammer for future compiles. And I can setup map-specific content mirroring scripts or bspzip instructions for each map, so everything stays organized and out of my game directory.
Kind of long-winded, but I'm excited for how this will work out.
