Yeah, understood, there seems to be a bunch of "yes, well, monkey with this thing" options, but if the default behavior is not to preserve all the resources because of some pearl-clutching paranoia or whatever, then it's not a complete web page now is it?
This is the worst gotcha I've ever seen
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.
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.