These apps have access to the iPhone UI patterns such as navigation controller, tab controller etc, and look and feel and work like native apps-- because they are native apps.
I'm tired of people who are ignorant of the technology and ideologically driven to spread lies calling the truth "bizarro world". You're the one who is telling the lie here, buddy. Your need to characterize me like that stems from it. Further, your ignorance of the existence of a solution is not proof that the solution doesn't exist, and when told about it, you should research it, not characterize me.
I write iOS apps for a living. I know how their distribution controls work, thanks. Without Apple's explicit permission for each and every device I can't distribute my app. To muddy the waters here is intellectually dishonest. You should be embarrassed for trying to argue that this is anything remotely like Android or any of the current desktop platforms.
How do I put executable code onto my iPhone and run it without their permission? Unless you can answer without the words "iTunes app store" or "jailbreak", you have proven yourself wrong.
Apple controls what goes into the store because they want to protect users from apps that steal information. iOS does not have the malware problem that android does as a result.
Javascript does not have the ability to do this, and so Apple will let you install wahtever app you want, directly from the safari browser.
It is not apple's fault that this has not proven as popular in the makretplace as the appstore-- but they had this feature in from day one, a year before the appstore even shipped.