When exercising, does the amount of effort determine calories burned or the actual work being done?

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Will an athlete who runs for an hour at moderate pace and is not tired at the end burn more calories than an out of shape person who runs for an hour a way shorter distance but is exhausted at the end?
Assuming both have the same weight and such

What I want to know basically is if your body gets stronger will it need less energy to perform the same amount of work?

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