Its writer actually used so many chained clauses that they ended up with a syntactical error... in English you can't say, "Although it isn't low enough by itself, but it is such-and-such."

It's tricky in the sense that anyone could get away with saying, "Although it isn't x, still, nonetheless, it is y," which means the same thing as, "Although it isn't x, it is yet y;" and, in some contexts, 'yet' and 'but' are allowed to be treated as interchangeable synonyms.

They probably just didn't have enough time or energy to finish the thought with enough attention, and punctuation has such usage conventions in order to let it aid rather than to confuse comprehension and attention. Commas are deceptively easy to get into without overhead, but not to get out of without it. We could simply abuse the commas and still choose either one of the following thoughts, but the Register ended up splitting the difference:

At $0.078 a kilowatt, Phoenix's power isn't as cheap as Washington State['s], which is closer to $0.04 a kilowatt, but it's still competitive, Howard said.

And, Howard said, while Phoenix's power, at $0.078 a kilowatt, isn't as cheap as Washington State['s], which is closer to $0.04 a kilowatt, it's still competitive.

Also the proper unit is kWh rather than kW.