The immutability of the OS is not, alone, meant as an in-depth security measure. Don't run malware as root. If you want a fully trusted boot system, you'll have

The immutability of the OS is not, alone, meant as an in-depth security measure. Don't run malware as root. If you want a fully trusted boot system, you'll have to use features like Secure Boot to verify that the BIOS and bootloader have not been tampered with. ostree supports signing commits and trees with GPG signatures, and like git, all objects are content-addressed by SHA256 hash, so it is possible to verify that the entire root tree and all objects within it have been signed by some trusted party.