This seems like something that shouldn't be the container formats responsibility. You can record arbitrary metadata and put it in a file in the container, so it's trivial to layer on top.
On the other hand, tie the container structure to your OS metadata structure, and your (hopefully good) container format is now stuck with portability issues between other OSes that don't have the same metadata layout, as well as your own OS in the past & future.
Honestly, sometimes I just want to mark all files on a Linux system as executable and see what would even break and why. Seriously, why is there a whole bit for something that's essentially an 'read permission, but you can also directly execute it from the shell'?
Maybe non-UNIX machines I suppose.
But I 100% need executable files to be executable.