Changes to the tree and restarts were are taking effect.
The root cause of this may be this:
The .1 location doesn’t exist anymore. There are two .0 locations. I’m wondering if this was due to upgrading to Fedora 32.
Probably relevant is that I had this issue from running livefs https://jlelse.blog/dev/fix-broken-silverblue/ . The livefs command was run after a few update failures to test and see if that would work.
After looking at grub configs, this bug still exists as well https://github.com/ostreedev/ostree/issues/1009 . That seems unlikely to be related. Still, it isn’t clear if the /boot/loader/entries are correct. There is only one entry in that directory now, ostree-2-fedora-atomic.conf. For whatever reason, there is another one created in the /boot/efi/EFI/fedora/grub.cfg file that also points to the :0 image.
I could manually perform filesystem operations to make the dirs, but don’t know if that is the correct way to go. Does ostree have a clean way to fix this?