...They will eventually incur one of three costs: reprocessing, geological storage, or release.

How much does it cost to maintain the current facilities? By what factor does it make nuclear energy more expensive?

I don't understand how automation changes the energy, material, or complexity costs (think supply chains or fuel flows) associated with a technology.

The most important component of economic cost is human labor. We have plenty of energy and materials in the universe left. "complexity" is not a limited resource so I don't understand what "complexity cost" is.

Some things will turn out to not be possible...

Yes, but I think that current technology is very far from the limits of the possible.

Except that when we look out into the universe we don't see Dyson spheres, or evidence of replicators from elsewhere having passed our way, and we would be able to see Dyson spheres from quite a distance.

Sure, because we are the only intelligent life the universe. What's so surprising about that?