Default settings for HTML purifier and how to extend it
Craft won't merge your HTML Purifier config settings with the default ones, but the default ones are pretty simple, so I'd just include them with yours.

{
    "AutoFormat.RemoveEmpty.RemoveNbsp": true,
    "Attr.AllowedFrameTargets": ["_blank"],
    "HTML.AllowedComments": ["pagebreak"]
}