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
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
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.
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.