I get your point but the risk of this becoming widespread enough that your nightmare scenario could happen is zero. It's not a standard way to use binfmt_misc,

I get your point but the risk of this becoming widespread enough that your nightmare scenario could happen is zero. It's not a standard way to use binfmt_misc, the only people who do are going to be nerds like us so on their own head be it. Plus regular users wanting to open PDFs et al will do so in the GUI rather than command line. The GUI has its own checks to make double clicking safe. However I do take your point that if for some bizarre reason Ubuntu and derivatives did start configuring binfmt_misc to open documents and recommending users getting into the habit of setting the executable bit on docs, that would be a bad thing.