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I don't think I've heard about some boot-time checksum verification of root partition. Doesn't mean it does not exist, just that I can't help here
My point is: if OS is not encrypted, it can be modified. And that verification idea, if is not stored under some encryption, could also be changed. Which means that by the time you put in your password to decrypt your home, you might be already running system that will nullify the protection. Encrypting your drive will only protect you in scenarios when someone snatches your device turned off