The files in the `/boot` directory are from the first partition of the SD card that's been mounted there during the boot process. Because the first partition is formatted as a [FAT filesystem][3] the files don't have the same meta-data available as when using, for example, the ext4 filesystem.

The [mount][1] command used to mount the partition has to somehow map the meta-data expected by the underlying filesystem from the mounted filesystem and this ends up with some of the flags being meaningless or mapped to different meanings. In your example, the [File Allocation Tables][2] on the SD card has no concept of a file being "executable" (I believe that actual vFAT systems look at the file extension to figure out if it's executable or not: it's a function of the OS, not the filesystem) so *all* the files will have the executable bit set when mounted.

There are other features missing in "vFAT" that can lead to odd behaviour when being mounted, such as no UID/GID; coarser timestamps that start at a different Epoch and restricted filenames for example. You can adjust how some of these are "handled", look at some of the options listed under the "_Mount options for fat_" section in the `man 8 mount` pages.

See also https://en.wikipedia.org/wiki/File_system_permissions#Operating_system_variations

[1]:https://linux.die.net/man/8/mount
[2]:http://www.tavi.co.uk/phobos/fat.html
[3]:https://en.wikipedia.org/wiki/Design_of_the_FAT_file_system