There are some things that are only available in Shortcuts because Apple gave the app entitlements to communicate with parts of the system that an AppleScript or other apps can't. Things like setting/getting the Focus Mode, changing some system settings like Airdrop Receiving, Color Filters, Background Sounds etc.

Also some apps export Shortcut actions that can run in-app code: for example my Lunar app has an action that can help fixing arrangement when monitors flip around [1]

It's much easier to implement a struct for a Shortcut, than exporting AppleScript sdef files or creating IPC command-line tools, so a lot of apps take this route for code that needs access to the memory of the running app.

[1] https://lunar.fyi/shortcuts#fix-monitor-arrangement

Apple designed Shortcuts to look like a shiny toy demo, and it gets awkward fast once you leave the happy path. AppleScript is old, weird, and still wired into a lot of Mac apps, but the moment it trips over something basic like text encoding you can lose an hour digging through forum posts from 2004.

With Hammerspoon, you get Lua and direct macOS APIs, so you can push much further if you don't mind writing more glue code. If you care about serious Mac automation, you'll probably mix them and curse each one for a different reason.