While I wouldn’t want this to be a general statement: platform-owned apps can be really terrible. Why? Because they don’t permit level-playing field competition between their own apps and third party apps on their platform. And that lack of competition is costly; maybe even for the platforms themselves.
Consider a first example: iTunes. iTunes is an app that exists on Macs and PCs that holds Apple sold content. When it first appeared alongside the iPod, there were some music players around but iTunes did its job. But a decade later and I cannot for the life of me work out what iTunes is for. It still holds content but that content is varied. Music, podcasts, television, movies, home movies and mobile apps — just mobile apps, desktop Mac apps have their own app store. And recently, it also holds Apple Music. But it is hard to imagine that this is any way close to optimal. For starters, why aggregate? How does that help the user? Second, why not think about personalisation? A list of playlists doesn’t cut it. In reality, it is some form of interface to cloud based content storage. Then why package it this way. Once you have the cloud you can lock the content so why not let others work out how to present that to consumers?
Let’s turn to a second example: Kindle. You don’t think of this as an app but it is. It is on multiple devices and plays the critical function of allowing you to read digital books. When it first appeared the sheer novelty of digital reading was enough but today as a reading app it is stale. There has been little innovation. And from a design perspective, there is little delight in a new page. Craig Mod, a noted designer, has explained how and why digital books have stopped evolving. The bottom line is apparently DRM but, in reality, I think it is because market power both on Amazon’s part in this space and from publishers has translated into just not caring. The lack of innovation has not only failed to keep track of reader expectations but has also lead to little innovation in book presentation itself. The combination is a tragedy.
Finally, a third example: Twitter. A few years ago, Twitter closed its platform (mostly). Apps were allowed that accessed Twitter data so long as they didn’t get ‘big.’ If that happened, then Twitter would pretty much ‘own’ them. But, as many have pointed out, Twitter is struggling with growth; mostly because people don’t know how to use it but also because Twitter itself doesn’t seem to know what it should be used for. Now Twitter did this, most likely, to keep control over potential monetisation. But the cost is enormous because it was apps and users that generated most of the significant Twitter innovations (like the famous ‘re-tweet’). For my own perspective, I doubt I would use Twitter at all but for Tweetbot (one of the pricier Twitter clients). It is precisely when a use case is ill defined that you want to encourage platform experimentation and innovation. But Twitter shut that down and is paying the consequence. And its own apps offer no path forward.
I say all of this to highlight a theme but also to argue that for some platforms the cost is worse than others. Sadly, it is hard to come up with a convincing business rationale that allows this state of affairs to continue and certainly impossible to come up with one that squares with the seeming damage done to user experience.
Digitopoly 
My first ebook reader was a Nook because, for unrelated political reason, I prefer Barnes and Noble. But the Nook drove me crazy with its terrible software and even worse technical support. Another thing I grew to hate about Nook was the B & N policy that books could be bought only while I was physically located in the United States, but at least they could be delivered anywhere. As a long-time computer techie, this limitation was trivially easy to bypass, becoming only an obstacle to those willing to conform to the limitation. In other words, it stopped only the ‘honest’ people.
Then I bought a Kindle. It was an early model and I hated the tiny buttons and especially hated having to use the arrow keys to move a cursor around to select any special characters. But I quickly discovered that Amazon would sell me a book from anywhere I happened to be. (Why couldn’t B & N do this?)
Then came both the Nook and Kindle apps. I even more quickly discovered that both of the apps were dramatically better than the physical devices which I only rarely used any more. Once I bought the iPad, where both apps are available, I entirely stopped using the physical devices and eventually wiped them off and gave them away.
I’m an American Expat, living in Taiwan. Books in English are in very limited supply and, for the most part, neither B & N nor Amazon will ship books to me here. I can get them shipped to a friend who handles my US mail, and he can resend them, but the cost is VERY high so I only rarely resort to this if a book is simply not available in ebook format.
So, unlike you, my reading is more and more concentrated into ebooks of which I now have several hundred. I love both of those apps and when I stumble across a book recommendation, it’s so easy to just buy a copy without knowing exactly when I’m going to read it.
Here in Taiwan, I teach pro bono English classes, two of them based on books available from Amazon. I have discovered that, with the exception of exactly one text book, I can open a book on several devices at the same time. So when I teach, I bring my Android phone, my iPad, and two Windows laptops all of which I can pass around so those who have not yet bought the book can participate. Effectively, Amazon has given me multiple copies of the same book. I know they can restrict this, because of that one text book that refuses to open on even a second device. So, as long as they allow me to, I feel they are implicitly authorizing this. (I do not dare to allow this to anyone outside my teaching environment because they could all buy books at my expense.)
When I moved to Taiwan in 2009, I got rid of most of my library but I still have about 400 physical books. It’s rather difficult to find a book even when I know it’s there, somewhere. But on the Kindle and Nook, finding a book is simple. If I could, I’d convert all but maybe 50 of these to digital if only I could.
While you make the claim that anyone can produce a physical book and distribute it world-wide, you have not considered the physical distribution costs that can easily exceed the cost of the book itself. Then there is the rather long time that distribution takes. There is one really huge bookstore chain in Taiwan, eslight, and I’ve been to several of their locations, but English language books are very very limited.
So, in conclusion, I have to disagree with you almost entirely. The Nook and Kindle formats have pretty much saved my sanity. I’d be going stir crazy in my retirement if I didn’t have these apps.
One short comment on your view of newspapers on the Internet. I subscribe to the New York Times. I have a home-delivery subscription that I give to my sister in California because it’s only a little more expensive than digital-only. But I read only on the Internet. Yes, the layout of the NYT is very different on the Internet than it is in print and I rather hate it because when I open the ‘current’ edition, it’s mostly old articles and I spend almost as much time looking for the new articles as I do reading them. I HATE this ‘wonderful new on-line format; easily as much as you love it.
I read the Craig Mod article to be sure I understood what you were referring to. He’s clearly in love with the books as physical objects. I have only a very few books like that; one being a very old book on mechanical drawing that I used in a High School class and but the gypsy touch on. But Mod did not consider that his beloved book on Rome will be substantially outdated if he ever visits there. I hope he buys a new copy before he goes.