The quote I like is "The only intuitive interface is the nipple, every other one has to be learned"

So as long as an interface is consistent with prior interfaces I guess it is "intuitive"

I have never used mac, but it sounds like a good interface to me, not the .dmg one, that one is. weird. but where the application is self constrained in it's own directory. The traditional unix method where the parts go according to their function (/bin /lib /share and all the /usr variants) is fine when all the software is system software(promotes reuse) and sort of works when you have a sys-admin whose job is to incorporate third-party software as system software(central package systems also fit this category), But it really starts to stink when you have independent third parties packaging their own software.

Another way to think about it is what is the best hierarchy function/application or application/function

Intuitive designs are nothing more that applying prior knowledge. I have to create simple next, next, finish instructions for people to install on Windows.

Example of this would be the ability to open a can of soda. You can do it because you saw someone else do it. Now give the can to an Amazon tribe that never saw the can nor how to do it before.

Windows uninstallers also do not clean up the system and leave trash everywhere. The registry is often the most litter filed area. Even Microsoft's _cleanmgr.exe_ does not fully clean your Temp folder and a manual removal is needed.

As a user of a number of systems; Mac installation is the cleanest and most simple. Linux's closest would be AppImage packaged applications.

Windows is one of the worst because often they are un-scriptable and require the end user to always interact. Mac and Linux can script their installations with ease. I'm saying this as someone that needs to manage systems which are air-gaped and service by others.