I don't see why it should be trying to remove /boot anyway. Say - stretching a point admittedly - /boot was empty because the /boot partition was unmounted, and this was somehow being run from a chroot or something weird, then it might remove /boot and cause a problem? Several packages use /boot so why does the kernel think it owns this directory? But if the situation never arises, as a lack of previous bug reports might show then - whatever.