Yes, if you don't customize the grub scripts to change the order, the top linux version is the main one.

I can't explain what you are saying about grub.cfg, it doesn't make much sense. If sda11 is your top version, then only the grub.cfg on sda11 should matter. When you run update-grub the os-prober does search for boot files of other OSs and makes an automatic entry for each found. All these entries go below the memory test entry in the boot menu (by default, unless customized).

update-grub usually does a very good job and that's why editing manually grub.cfg is not recommended. You can do it for troubleshooting purposes, but carefully. If you are not 100% sure your grub2 on the MBR is from sda11, you can try booting sda11 and running:
sudo grub-install /dev/sda

That will install it linking it to sda11.

We haven't addressed one important question, the UUIDs. Did you confirm you have no doubled UUIDs for the recovered partition? As I said, I don't know exactly how clonezilla does it. Have in mind that it's not designed to restore on the same disk next to the original partition. If the clonezilla restore uses the original UUID, that would mean you can end up with same UUID for two different partitions which will create confusion for both /etc/fstab and grub.cfg. Check the UUIDs with blkid and make sure sda11 and sda12 have different one.