When creating a new project and choosing "Save", PHPEd starts out by offering to save the project in the "Projects" folder instead of the configured "Project Root folder".

This matches the default project layout, but does not match the layout where you keep the project files close to the source files.

Could the "use project root folder as default project save folder" be added as an option, unchecked by default?

I'm not sure why would it offer project root as default
Personally, I would not like stuff like .ppx, .ppj, .ppd to be published on to my live site as part of the project.
Do you have a strong reason to keep .ppj file (a other helper files) in the project root?

This project organization resembles the one that MSVC and similar products use, and keeping with this system is a benefit when working on multi-(programming-)language projects.

Putting the project files in the root folder is not nescessarily desired; most often they'll be located in a 'phped', 'projects' or even 'win32' subfolder, the way it's done in many projects with regards to other IDEs (id3lib, boost etc.), for instance:

Also, this makes for easier version control repository maintenance and backup, as all files are kept in the same tree.

Publishing the project files is not an issue thanks to PHPEd's excellent "exclude" features.