There is a file
gtk.gresource in the same directory. It contains all packed theme files.
resource:///com/ubuntu/themes/Yaru/3.20/gtk.css refers to
gtk.css file packed inside this file.
You can view a list of all packed files with a command
gresource list gtk.gresource
You can unpack a particular file using a command eg.
gresource extract gtk.gresource /com/ubuntu/themes/Yaru/3.20/gtk.css >somefile.css
Note that the contents of the file is extracted to stdout so you have to redirect it to some other file.
I don't know however how to pack the files again into
gtk.gresource after editing. But you don't have to pack them, you can unpack all files from
gtk.gresource file and leave them in unpacked form.
I recommend however that you don't edit the Yaru theme in place because your changes might be overwritten when the theme's files are updated. Make a copy, change the theme's name (you must edit
index.theme file in theme's main dir) to something that is unlikely to be used by standard themes (I use "My Theme" for example) and edit the copy.