With Flash, the user or the developer has no choice if scroll and keyboard shortcuts break. With JS+HTML+CSS, the user has a choice to force the developer to fix their code (and a developer to not write code which breaks browser stuff).
In Flash, browser shortcuts like ^L are always broken and you have no choice about that, because that's the way Flash is designed. If a similar thing happens in a non-Flash environment, it's because the developer designed it so.
If many users complain to the developer about stuff being broken, it has to count for something.
Again, how do they "force" developers to fix their code? Asking nicely is one thing but forcing is another. You implied that the user has more control over the developer in a JS+HTML+CSS environment over Flash. Plus, if some commonly used commands are broken in Flash then it's broken in all of them which doesn't mean broken; it means unsupported, there's a difference.