Items not explicitly in prefs.js have default values. A preference
variable with a default value will generally not (will never?) appear in
prefs.js, but the Mozilla software detects its absence and assumes the
default value. For preference variables with default values,
"about:config" shows what the software will use.
You can "create" a preference variable with a non-default value. Then
it will appear in prefs.js. If you then change its value to the
default, it will be removed from prefs.js but still show in
"about:config".
If you wish to extract ALL preference variables shown by "about:config",
you need an extension that captures the "about:config" display. I just
tried, and the display cannot be printed. Thus, "printing" to a file
(e.g., PDF) will not work. Instead, you need something that will
capture the display as it is generated, not afterwards.