If you dual boot Arch Linux and Windows, your /boot partition is outside the / partition. This answers your question why the /efi directory is not backed up. You can back up your root directory and your home directory. I also assume that you do not have a btrfs system, which is why you use rsync. Normally one mounts the EFI partition as /boot/efi. I use btrfs, it is better and gives you more finesse when using timeshift. Rsync snapshots contain only those files and directories that have been changed or modified.
To restore the /efi partition you boot into arch using the install disk, mount the /root and /efi partitions and then chroot. That would be the way.
Why not rsync your EFI partition by hand? Or write a simple script? Timeshift is limited in it’s use and many people say, it is NOT a backup-program for the exact same reason you are posting your problem.
I just made an rsync snapshot of my system with Timeshift.
My ESP is mounted at /boot/efi.
I can verify that the content of my efi folder residing on that partition is all there.
So I don’t really understand the issue here.
If you make an snapshot and choose to include all the files in root, then the content of efi directory should also be included. If it is not, go to settings and Filters tab. At the bottom click on Add Folders and add whatever folders you want to be included in the snapshot.