The folder structure for Publish output is set to use your output folder as the parent directory, then with the project name and file type inserted as you see.
I imagine "the thinking" is that you can generate multiple types of output for multiple projects without having to shuffle to various directories.
However, if you "only" have one output type for a single project, it does seem to be overkill.
**To avoid the additional layers of organization, use the File > Save as PDF option, which uses the current Publish panel settings. In this way, you can select the directory you need. In my experience, especially when the PDF is saved to your project directory, it sort of becomes the default location for saving, so you don't need a ton of navigation to identify the directory after you first save the file.
-Matt