The chakra in the Rinnegan he possessed allowed him to do all he did against Naruto despite being virtually dead.
If his body was in the same condition as after he absorbed Bees chakra with both Rinnegan containing Hagoromo's chakra, then he'd be Capable of far more than he ever showed.
Nagato never had Rikudo chakra, the Rinnegan was simply stated to have an immense chakra. The body itself has Rikudo chakra flowing through, as in Madara's body, as he mixed Ashura's and Indra's chakra.
- What was shown in his strongest state is, his CT is trash to PS, as it can't even bust it, nor is it taking multiple strikes from Sasuke's end. ST is withstood with little difficulty, PS is too sturdy to be knocked over by it, let alone majorly damaged.
- Preta is nigh useless here, never coming in close contact with Sasuke, nor is it absorbing any of Susanoo's physical attacks. Rest of the Paths hold zero value here, and especially considering he's Edo, he can't even summon the Mazo, now that I recall.