That is true. The theme is set up so that only options that are set in the customizer or theme options will be output into the source code of a page. The defaults are handled in the style.css file.
You can still change any of them. I believe this is a list of the defaults that are green arranged by the tab in the theme options where you’ll find them.
Header Tab
Text Logo Color
Text Logo Color (hover)
Navigation Item
Navigation Item (hover)
Navigation Button Color
Navigation Button Color (hover)
Footer Tab
Footer Link Color
Footer Link Color (hover)
Content Tab
Link Color
Link Color (hover)
Buttons Tab
Button Background
Button Background (hover)
Hope that helps out. If you can’t find a green that you’re trying to change, let me know where it is on a page you’re working on and I’ll point you in the right direction.
Thanks,
Bill