However, getting people used to double extensions is one quick way of increasing the success rate of attacks such as the infamous “.pdf.exe” invoice from an email attachment.

Very good point. Though, i would argue that this would be much less of a problem if Windows stopped sometimes hiding file extensions.

I can’t see how Windows’ convention is worse

I don't believe what you're referring to is really a Windows versus Linux/Unix thing.

If I zip a file, it doesn’t matter what it was in a previous life, it’s now a zip - this is also how Unix deals with many filetypes, I’ve never seen a .h264.mp4 file, even though the .mp4 container can actually represent different types of encoding.

I disagree, but i do get what you're saying here. I don't think that example really works though, because a .mp4 file isn't derived from a .h264 file. A .mp4 is a container that may include h264-encoded video, but it may also have a channel with Opus-encoded audio or something. It's apples and oranges.

Also, even though there shouldn't be any technical issues with this on Windows, you can still use a typical short filename suffix if you wish, though i would argue that using the long filename suffix is more expressive. From "tar (computing)" on Wikipedia: