So, now I have tried to run these commands:
sudo rpm-ostree upgrade # I don't know if you NEED sudo
sudo ostree admin finalize-staged
sudo grub2-mkconfig
Rebooted, and everything seems to be going well. I read about these in this thread, and another here, then over at these two GitHub issues for rpm-ostree/3925 and fedora-silverblue/322. I also found a blog someone wrote which talks about how they fixed this as well, here. Whether or not these actually fix the issue is something I don’t know, but they make it so the updates successfully take.
I generally try to not layer on more packages than I need for Fedora Silverblue. Everything else is done through the Toolbox or Flatpaks.