Eschema and PCB were separate programs that were merged. Knowing this helps to partially understand the structure. It is being reworked for the next version release.
Generally Kicad loads a default set, but not all, libraries. On a slow computer loading all can take a little time so that's why the default behavior is not to load everything. This can make you believe 'stock' parts are missing when they simply haven't been loaded. Look at your library paths in Eschema to find out where they are located. Open a few. They are text files. When you create a new part you generally want to make a new lib in your name space for it. Before saving new parts you have to set your private library as 'current'. You also have to make sure it is in the list of libraries that are loaded.
The PCBnew stuff will be separate but the same principles apply. I have no idea how much this changes when version 5 comes out. That draws closer.
The good thing about text files is that in the beginning I was creating a new lib for every new part because I was offered the choice. I went back and was able to do cut and paste and make one file out of it.
Also, keep in mind English is not the native language for developers so things that seem to have what you might consider an inappropriate name made sense to someone.
It may be quirky but it really isn't hard once you see what is going on and have done it a few times, but yeah, it is far from intuitive out of the box.