If you have a built a permissive kernel & SuperSU (zip) just keeps annoying by patching boot image for a system-less root everytime, you can flash this simple zip via TWRP (or CWM if it exists for newer devices). It will simply disable system-less installation method, and force SuperSU to do a system install.
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Note: Forgive the dots above. I just wanted some space because the post didn't look good before.
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Note: Forgive the dots above. I just wanted some space because the post didn't look good before.