You forgot to mention the part where Apple was first to implement features that later become known as HTML5. Also, the story of Web SQL and IndexedDB is not so simple.
Can you tell the story that explains why Apple has done nothing with IndexedDB for years while every browser vendor implemented it a while ago? Because the story as I see it is very clear: Apple embraced the web when they had very small market share, and they're doing the opposite now that they have a good chunk of the market. Walled gardens generally aren't very profitable if you have only a tiny fraction of the market.
Of course, it'll be hard for you to tell a convincing story because (AFAIK) Apple hasn't even commented on IndexedDB. Strange, for such a well-established open standard. Even MS has supported it for years!
My understanding was that Safari used JIT which is prone to security issues with how it executes that code.
As to why it's safer to do so in Safar that in a webview must be because the only API to safar is from the JS/HTML/CSS but with a webview you have a C/ObjectiveC API from the other side, which may be harder to protect against.
[EDIT] - More information on the topic from Gruber http://daringfireball.net/2011/03/nitro_ios_43 although there is no reason given as to why a UIWebView is more at risk from exploits than Safari.
This reeks of the same logic that caused them to disable HTML file upload buttons (there's "no" filesystem -- which is apparently why you can't even browse for photos and uploads until recent IOS).
This is what drove "there's an app for that" for so many years: Apple's systematic limiting of web apps into a severely curtailed walled garden so that the app store would -- in fact, could -- be the only source for real applications.
"Web Apps aren't as performant as native" is a direct result of such strategies.
In other words, those strategies WORKED. As with all anti-competitive practices, they will keep doing their job for a while, until something new and better (or at least workable) comes along.
What's extra fun is that when Steve Jobs introduced the iPhone in 2007, he explained that developers could write web apps if they wanted to create software for the iPhone.