They're listed in the Default File Settings - search for indent_guide_options
Stippled regions are not exposed to the API.
Thanks for the report, will fix for the next build
That's more or less working as designed, as ".sublime-project" is considered to be the same as a file called "foo": i.e., just a file name without an extension. A better option to create hidden projects is to call it ".myproject.sublime-project".
I'm unable to replicate this. What OS are you on, and do you have the open files hidden on the side bar?