Who cares?

There are tons of games in the App Store with custom user interfaces that don’t match anything from Apple.

Thats not the issue, the issue is that cnn or whatever.com might render differently or not at all if viewed in one browser, instead of the other. I dont know the internals of puffin, but security and js attack vector, might be different as well.

You said "and therefor visually could/is rendering differently than safari/webkit"

You didn't say anything about security, but there is no security problem either.

The client side wouldn't be evaluating JavaScript outside of Apple's JS engine so there is no security risk whatsoever.