With a block device copy approach like in TFA you don't need to worry about that because those filesystems do not exist on the block device.
When copying files (e.g. with rsync) you need to watch out for those, yes. The best way to deal with other mounts is not to copy directly from / but instead non-recursively bind-mount / to another directory and then copy from that.
When copying files (e.g. with rsync) you need to watch out for those, yes. The best way to deal with other mounts is not to copy directly from / but instead non-recursively bind-mount / to another directory and then copy from that.