I get where you’re coming from. I suspect that much of that flexibility was never intended. After all, OS X started as a workstation OS for a different market than Apple entirely.
I won’t address your whole comment but I feel compelled to point out that Music is iTunes. The Music app was just a name change, and, confusingly, Apple Music (the service) is an entirely different entity than Music (the app). Your own local music files (either your own MP3s or iTunes Store purchases) are still accessed in the same iTunes Media Library folder as they always were.
Music was just a rebrand, and it spun out podcast, audiobook, and iPhone/iPod sync. But the rest of it is 100% iTunes.
I don't think enough people appreciate just how beautifully hackable OS X used to be. The Library folder was unhidden by default, basically inviting users to go explore their systems. Applescript and Automator were treated as first-class citizens, offering an easy way to extend existing apps. Custom themes—while never officially supported—were easy to make via a bit of file replacement, and there seems to have been quite a lot of them, if DeviantArt is any indication. And there was nothing to stop you from writing and loading your own drivers to add support for new hardware, as plenty of enthusiasts did.
Today, stock apps like Music store data in obtuse and non-human-readable locations, Apple Events are virtually useless due to mandatory permission dialogs, kernel extensions are deprecated, and the root filesystem is mounted via a complex snapshot mechanism in which a reboot is required for changes to take effect.
Perhaps this was always Apple's goal. Perhaps it was necessary for security. Perhaps, for a majority of users, it ultimately provides a better experience. But if you are someone who likes to tweak and customize your machine, OS X used to be a great home, in a way that it isn't today.