The gutter icons paths are hard-coded, as you’ve noticed. The main reason for this is that the current gutter drawing logic isn’t aware of the theme system, and isn’t able to export elements to be themed by it. It’s also worth nothing that the gutter icons have some post-processing applied to them, so they’ll be tinted to the same color as the region added via the add_regions API.
The icon name is an argument to the add_regions API call, and may be dot, circle, bookmark or cross (although it reality name will work as long as there’s a corresponding icon in Theme - Default).
The fold marker path is hard coded for a similar reason, although it doesn’t have the tinting applied.