I'd like to offer my very personal ideas of explanation (essay) to the question, why there are non intuitive OS by commercial publishers.
And I like to put my focus on MS Windows, because I don't know Android and I find Apple's Mac OS (at least the older version) not as such not intuitive at all (there are many other issues against fruit, but leading off-topic.)
At first it's hard if not impossible to really hit the target of what everybody experiences as what intuitive is. Design a one-size-fits-all actually means it does not suits anybody perfectly really.
A turnkey OS or to be more correct a desktop environment is a forethought collection of ideas about thinking structures. If your thinking is structured otherwise you cannot be satisfied with it.
For small and simple systems, such like smartphones or other devices with only a few functions, this ain't no big deal. But with a computer everybody has a many different jobs to do. So a one-size-fits-all even must fail if you get the same (G)UI for CAD, IDE, writing Text and configure the system.
But this wouldn't be a real problem if four points are met:
1. Design it as logical and intuitive structured as possible from the start
2. Make it as customiziable as possible (including offering completey different UI possibilties [shell/desktop])
3. Improve it, make it better
4. Make it worth to learn it
FreeBSD meets all four points of it, being fully aware that point 2 cannot be matched if you stay limited to full automatically self-configuring single-user-desktop-game-launch-and-a-bit-office-turnkey-OS, and 4 also means: if it's worth to learn it, the users learn it, thus opening way more option on 2.
There is an inharent trap.
You cannot have all: Full customizations, so meeting maximum of personal intuitive usage, thus meaning more than just shallow control and system's configuration, and closed code for commercial software. Neither as less complexity and most easy use as possible is disparate with adaptivity, flexibility and customaziablility.
One have to find a compromise. And this for itself is a major part of customazition already.
Microsoft takes this burden from its users and decides how the compromise for their customers looks like.
This is a trap for customers/user. For a commercial publisher like MS it's an opportunity.
Microsoft does not do any of them four points. Customers are suggested that it seems, but it's not.
As they launched MS-DOS and later Windows 3.11 much better logical strutures and intuitive usages would have been possible at that time as shown on already existing other systems and by respecting basic laws and experiences by over 40 years of computer science and UI.
And they didn't made it better. Windows became larger, got more features, became more colorful - faceliftings ("sex sells"), maybe more powerful.... and it's usage changed, but it did not became better, neither in usage, and especially not in intuitive usage.
You may see it e.g. at system's messages. Within a unix-like open-source OS the system produces understandable messages, telling what's up, at least you can retrace them, learn what it means and you have a chance to solve the problem yourself. (Since I don't use any desktop environment but a simple fvwm only, my system does not produce any unasked messages at all, except on e-mail income or when I actively do anything. Otherwise it stays totally quiet and completely silent. It's heaven!)
Windows system's messages can be put into two categories: At first you have "OK-Messages". The computer informs you about anything (mostly inforubbish), and you have no choice but "OK" only. They seem to give the user the feeling of the computer is working and doing a lot for him. But in fact they're forcing the user to react, turning the whole idea of computering upside down by making the machine master and user the slave, stealing user's proactivity, killing his creativity, thus topedoing intuitivity. The user don't need no actual task what to do with the computer, but is kept busy and has the feeling having done a lot with it.
At second most Window's error messages are a complete own computer's gibberish. One has to read them several times suppressing headaches while trying to get any useful clue from it, only figuring out most often there are non. In many cases it's just empty verbiage to impress and put off the user. Most Messsage are a subtle way to tell user:"FU! You're too stupid to get it anyway. Knuckle under and consult somebody else who knows!"
That puts off user to learn the system and much more preventing them to even think of touching other systems. Because even the most ignorant user sees on the very first look: "Other system, other gibberish. I don't get this either. Especially not if it's more text, but just clicking buttons with the mouse."
The customization is restricted to very few minor points only, such as colors and themes - from those you get endless ("Wow! How configurable this system is!" No, it's not. You just can chose infinite looks for the same usage and structure. Best example how's the most user's mood: Putting a picture as desktop background. Pictures and even changing/animated backgrounds actually kill the clearness, are distracting and so lowering the productivity. But they look cool and one can express himself better as with a boring plain background. And if nothing else is to do, one can look for an new background picture aka "work with the computer")
And instead of doing a continuous improvement with every new version of Windows there is a complete new design particulary of the structure of usage and what is where, and how it's named now.
Thus making it unworthy for any user to get actually into it, even it's shallow.
With every new version of Windows things change. Thus it's not worth to really learn it deeply, because in a few years a new version is published you're impelled to switch to. With any new version of Windows things you may have learned may not exist anymore, and several things are completely new you have to learn - and you don't know until the new version is published. And you don't know when even that happens.
Besides that Windows does not offer much depth for their users to learn and it's pointless to learn anything on a system that should be intuitively usable anyway. And if this version is not, the next should be.
So most users don't really learn the system because it makes no sense. They don't want to. They don't need to. They don't shall.
Thus keeping them stupid and dependent.
If you started with Windows, never seen anything else, you don't know better. You don't miss what you've never experienced, such as efficient working on a computer, high quality results or an OS you may understand and control.
If you see anything else, the first thing you smell is effort. And that's waht most users don't want at fewest at all: Even more effort with computers. Because on the OS which promises to be the most effortless to use they've learned, computering - learning computering - is tideous, annyoing. And any other system says truefully it needs learning. And you don't want/need burden yourself with an additional adventures not knowing if it's of any use/advantage, don't coming to the question: Learning once is enough.
So you stuck with it. Most because they don't know better. Being not happy at all, but don't change it, because they don't even know it could be better.
Because that would mean leaving the comfort zone you are placed in unasked, not being aware of how uncomfortable it really is, and how exploitetd and mocked you are.
(More people start to smell a rat since you must pay periodically instead of buying one license for a lifetime.)
Additionally all this gives Microsoft backing support from third sides.
An imperfect system needs additional tools. So outside MS additional programmers working in additonal companies providing/selling additional software.
Anybody uses it, so anybody uses it.
An user of a not intuitively usable system depends on support. Taking classes, buying books and even if it's only the friend who can feel better about himself, because he is frequently asked to help.
And a system which leaps which ever version is also capable for planned hardware obsolence.
So you have a lot of people participating of it and of course not telling you:
"Windows is not good. Change the system!"
On the contrary, they try to ruin any alternative.
