No, the boot partition is not supposed to be mounted normally. Usysconf is supposed to mount it temporarily during updates but then is supposed to unmount it afterwards.
What likely happened here is that usysconf/clr-boot-manager will assume the partition is already mounted if there are already files in it and will perform all operations on the /boot folder as normal (which then are ignored since the actual boot partition is used). I think this can happen if you have the boot folder open in a terminal or somewhere and the mount fails, which is probably what happened in this case.
I'd recommend that you unmount the boot partition and delete everything under /boot (but not the folder itself). This will ensure that usysconf keeps it updated in the future.
