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It depends what you want... Lots of JS will not work offline and I don't think a plugin can know what will work or not. If the page is dynamically populated from an API, saving the page to rely on JS later could be basically wrong.

This is the worst gotcha I've ever seen

It's not paranoia, it's a feature that I consider to be useful and desirable. When I want to download the JavaScript, I use the built-in "save" feature. When I don't, I use SingleFile.