The cynical part of me wants to think that it's because by hurting it in WebViews and in a desktop-shortcut they can "support" these technologies without fear of them cutting into their app store sales/numbers.
But I have heard that there are some shitty technical problems with it.
Safari is not the same as a WebView when it comes to the code, and apparently a desktop-shortcut app runs in a WkWebView. So while they were able to add these features to Safari, the process of adding them to a WebView is much harder since it's intertwined with the OS so heavily.
According to someone I talked to a while back, WebViews and Safari in iOS are different enough that sharing code isn't exactly easy or straightforward.
But then the cynical part of me kicks back in and thinks that they shouldn't be following into the footsteps of Internet Explorer which hit the same traps and potholes (the integration with the OS meant new feature were extremely difficult to add, and the browser lagged behind because of it).