Apple is the origin of the modern mobile web. And you can publish a web app on the App Store if you want, and many do that. The rest is very much a matter of philosophy and design that goes well beyond "Apple wants to push the App Store".
The reason why Thoughts on Flash was removed is that... Flash literally doesn't exist anymore. It's not like the text is not preserved historically all over the web. I have a PDF of it even somewhere on my drive.
Please explain how that alone is a reason to make the richest corporation on the planet go through their whole online presence and remove a few kB of redundant text.
Nobody does that just because it's not needed anymore, it's more expensive to pay an employee for deleting this than just keeping it up for another decade. It's very obvious Apple wants to hide the fact Steve Jobs would disagree with their current way of doing things and fell for the Streisand effect as everyone does.
Yes you're right. Only small companies can delete a page.
What even is this sentence, it makes no sense.
I agree that this was a deliberate political move from Apple, but I call survivorship bias on the 'everyone falls for the Streisand effect'. Consider that you only hear about the ones the do get caught.