If your process is 30% efficient, it wastes 70% of input. If you increase efficiency 1000x, it wastes 70% / 1000 = 0.007% of input, so it's 99.993% efficient.
I'd expect the headline to resolve to some perspective where the numbers do make sense, in some very special, limited way, assuming that they didn't just roll dice to decide how many orders of magnitude to falsely claim.
Unfortunately, there's a huge crowd out there that combines, in a surprising way, radical science scepticism with radical science optimism. The "science said man cannot fly, then came the Wright Brothers" crowd who refuse all painful achievable improvements based on their hope for some convenient miracle. These headlines are dangerous.
The fact that no absolute number is given in the article makes me want to boycott it.