It does not account for a lot of things, for example insurance.

Quote from https://www.manager-magazin.de/finanzen/versicherungen/a-761... (Google translated):

Berlin – According to a study, comprehensive insurance against the risks of nuclear power would cause electricity prices to explode. According to calculations by actuaries, the premiums to be paid could cause electricity prices to rise more than forty-fold.

"Nuclear energy is ultimately uninsurable," said insurance expert Markus Rosenbaum on Wednesday in Berlin. If an insurance company wanted to build up sufficient premiums for a nuclear power plant within 50 years, for example, the remaining operating life of a reactor, it would have to charge 72 billion euros per year for liability insurance.

The German Renewable Energy Association (BEE) commissioned the "Leipzig Insurance Forums" to conduct the calculations even before the Fukushima reactor disaster. "The true costs of nuclear power are ignored and, in the event of a serious accident, are passed on to the public," said BEE Managing Director Björn Klusmann.

LCOE refers to the price in MWh (produced electricity), so it takes capacity factor into account. Whatever electricity you produce and sell depends on your installed capacity multiplied with the capacity factor.

Similarly, you pay for the electricity you receive and this is priced as say 40$ per MWh. Obviously when you receive nothing the price is 0, you don't pay them to idle, they either produce or not. Thus when storage costs kick in you don't add the costs of both together. You either pay one or the other, not both.

You might average them out taking into consideration what their output is, but you don't stack the costs on top of each other which I often see people do.