The author keeps questioning why certain siloing like App Store happens. The author then offers technical solutions that won't work. The reason is the siloing is intentional on part of companies developing those applications to reduce competition to boost profits. They'd rather provide the feature you desire themselves or through an app they get 30% commission on.
A lot of other things author talks about keep the ecosystems going. The ecosystems, esp key apps, are why many people use these desktop OS's. Those apps and ecosystems take too much labor to clean slate. So, the new OS's tend not to have them at all or use knock-offs that don't work well enough. Users think they're useless and leave after the demo.
The market effects usually stomp technical criteria. That's why author's recommendations will fail as a whole. "Worse Really is Better" per Richard Gabriel.
More benign versions of the same idea: app developers want to "provide a seamless experience"; they want their apps to be visually distinctive; they want to be portable across different OSes; they want clear boundaries between what they have to support and what they don't (is a copy-paste idiosyncracy something we have to document?); they can get performance advantages by implementing functionality themselves; and they're worried that the OS will change a critical subsystem or interaction in a way that isn't straightforward for them to adapt to.
This shouldn't be an issue on a free and open operating system, like Linux. Profit isn't a driver for LibreOffice or Blender, but these apps are still siloed off from each other. I think the author is right in that if the operating system offered both a richer and simpler set of tools to make it easier to add OS components and to communicate between applications, we could really see some interesting stuff.
Personally, I do find the idea of an operating system composed of services and applications that all share the same messaging statement compelling.
Profit is definitely a driver for much open-source software, Google pushes Android so they can control mobile advertising, Oracle pushes Java to stop Microsoft having a stranglehold on corporate development, RedHat pushes Linux so it can sell services. There aren't many big open source projects that are purely altruistic.
For sure there are projects that are driven by dollars, but many that are not... If we're going to get a desktop environment with the level of openness that the OP would like, I do think this would be a job for libre developers as it is fundamentally at odds with the pursuit of dollars via lock-in (that is, every app would be increasing the value of the OS and sacrificing lock-in of the customer's data).
I'm not seeing how products that are funded are "corrupted". I think that products that are funded need to make money and that drives the pressure to cordon off the customer's data and to lock them into the specific application. I'm not saying that this is innately bad (though some people might), but that it runs counter to this idea of building an OS that does more than simply launch software and store data. If you're feeling pressure to own the customer's data, then you won't be all that interested in making your application available to the rest of the OS by providing a suite of services.
Control of quality and auditing is another reason why apps stores exist and are useful: The (on average) high quality of the apps in the iOS store is the result of a rather strict auditing process, which in the end is also beneficial for the user. This is something that usually doesn't happen naturally with completely open systems. Even the Linux distributions (that are usually run mostly by volunteers and not profit-oriented) often have very strict criteria that your package needs to fulfill in order to be included in the official repository.
A lot of other things author talks about keep the ecosystems going. The ecosystems, esp key apps, are why many people use these desktop OS's. Those apps and ecosystems take too much labor to clean slate. So, the new OS's tend not to have them at all or use knock-offs that don't work well enough. Users think they're useless and leave after the demo.
The market effects usually stomp technical criteria. That's why author's recommendations will fail as a whole. "Worse Really is Better" per Richard Gabriel.