What "permission headaches"?
I know that it's possible to script that since Homebrew handles it automatically, but if you just want to use a specific app outside of Homebrew, experience is definitely worse than on Linux/Windows.
Things I prefer: Raycast + it's plugins compared to the linux app search tooling, battery life, performance. Brew vs the linux package managers I don't notice much of a difference.
Things that are basically the same: The dev experience (just a shell and my dotfiles has it essentially the same between OS's)
It may seem like a small thing, but when you have literal decades of muscle memory working against you, it's not that small.
What messes me up when I'm working on a linux machine is not being able to do things like copy/paste text from the terminal with a hotkey combo because there is no CMD-C, and CTRL-C already has a job other than copying.
IMO apple really messed up by putting the FN key in the bottom left corner of the keyboard instead of CTRL. Those keys get swapped on every Mac I buy.
I agree on the Fn key positioning... I hate it in the corner and tend to zoom in when considering laptops for anyone just in case. I've also had weird arrow keys on the right side in a laptop keyboard where I'd hit the up arrow instead of the right shift a lot in practice... really messed up test area input.
It's the same thing when switching from a Nintendo to a Western game where the cancel/confirm buttons on the gamepads are swapped.
But in the end the biggest thing to remember is in MacOS a window is not the application. In Windows or in many Linux desktop apps, when you close the last or root window you've exited the application. This isn't true in MacOS, applications can continue running even if they don't currently display any windows. That's why there's the dot at the bottom under the launcher and why you can alt+tab to them still. If you alt+tab to an app without a window the menu bar changes to that app's menu bar.
I remember back to my elementary school computer lab with the teacher reminding me "be sure to actually quit the application in the menu bar before going to the next lesson, do not just close" especially due to the memory limitations at the time.
I've found once I really got that model of how applications really work in MacOS it made a good bit more sense why the behaviors are the way they are.
The OS also has weird rough edges when used from the terminal - there are read-only parts, there are restrictions on loading libraries, multiple utilities come with very old versions or BSD versions with different flags than the GNU ones you might be used to coming from Linux, the package manager is pretty terrible. There are things (e.g. installing drivers to be able to connect to ESP32 devices) that require jumping through multiple ridiculous hoops. Some things are flat out impossible. Each new OS update brings new restrictions "for your safety" that are probably good for the average consumer, but annoying for people using the device for development/related.
You use nix or brew (or something like MacPorts).
And they are mighty fine.
You shouldn't be concerned with the built-in utilities.
I've had it make major (with breaking changes) updates to random software when asked to install something unrelated.
HOMEBREW_NO_AUTO_UPDATE=1
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
export HOMEBREW_NO_AUTO_UPDATE HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK
the workarounds on the internet are like "just build the image so that it uses the same uid you use on your host" which is batshot crazy advice.
i have no idea how people use docker on other platforms where this doesn't work properly. One of our devs has a linux host and was unable to use our dev stack and we couldn't find a workaround. Luckily he's a frontend dev and eventually just gave up using the dev stack in favour of running requestly to forward frontend from prod to his local tooling.
System-wide dependencies installed via home manager, and project-related installed via nix flakes which is created on project basis
I can spin up a new identical environment on new macos in 15 mins