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My understanding was that they don't want to allow executing downloaded code that hasn't gone through the App Store review (such as JavaScript in web pages). I think they allow Lua for scripting in games, though.

So, basically, a 3rd party JavaScript engine is not allowed. I guess you could write your own browser engine that doesn't support JavaScript.

I guess Flash was not allowed for performance and security reasons (lots of vulnerabilities, right?)

Alternative browser engines are forbidden, JavaScript or no JavaScript.

Steve Jobs wrote an essay why Apple didn't allow Flash on iOS in 2010:

Thoughts on Flash https://www.apple.com/hotnews/thoughts-on-flash/

That is an excellent question I'm afraid I have no answer to.