I miss ResEdit. Pretty much every Mac app in the day used the standard system for managing their resources, so you could pick apart anything with ease using ResEdit. I don't know of any modern equivalent for Unix/Windows/Mac programs.
Also, regarding "burned-in configuration" resources—those are now found in the app bundle's Info.plist :)
In some sense, I think it has deepened the digital divide.
I think the issue is not so much "command line hides power and treats GUI like a second-class citizen", though that is true, but rather that preferring one over the other creates problems.
This issue is again rearing its head in website design - many "web applications" have states that are not reachable via linking.
Nowadays on macOS, with the availability of the CLI, Apple engineers have decided to expose those same effects through CLI utilities that call directly into private system APIs (which are themselves usually client libraries for private Mach client-server ABIs.) If there's a switch exposed in the GUI but not the CLI, it's unlikely there's an event to reach it any more.
(Though, in macOS or Windows or Linux, it's always a possibility to write a script that has GUI effects directly in terms of "click the first button on the right"-style accessibility directions. But that's extremely brittle to system version updates, and precisely the thing that exposing an automation API is meant to avoid.)
You're right that a lot of GUIs aren't designed for automation, but CLIs aren't the only answer. Classic MacOS had a powerful scripting architecture. (It still exists, but it's been neglected.)
If you could, I think most developers didn't, since AppleScript isn't a default means of using the computer the way Unix shells are.
Command line interfaces are powerful, yes, but they're also a crutch. It's very easy to hide certain features by exposing them only through command line flags or what have you. On classic Mac OS you could not do this; you needed to attach every feature to a GUI control of some kind.
As a consequence, people came up with all kinds of GUI tools for pro/expert users. Linux, comparison, treats GUI users as second class citizens and tends to relegate them to only the most basic functionality.