The root CA is a self signed cert while the intermediate is signed by the root. On the clients only the root cert has to be installed to verify cert paths. So the root is your trust anchor. The private key for this one should only be stored completely offline to protect it as good as possible from attacks. If something happens (you loose the control over the intermediate private key) you can grab your root and sign a new one without touching the clients to delete the old and install a new root cert - which would be required when you loose controll over your root CA private key.
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