That’s why I asked to dig deeper in your memory. 
No, that has nothing to do with the boot flag.
No, that’s for your LUKS2 encrypted /, I reckon. BTW, I see no /boot there for an unencrypted boot partition. You should be aware that’s not exactly standard and may cause issues with future release upgrades or make them impossible altogether.
Does that alter /etc/fstab?
BTW, what even is your filesystem layout; it didn’t seem relevant at first, but now I’m curious:
lsblk -fe7