The key word: "application". It is the application of combustion that is not 100% efficient. Just as the application of nuclear reactions is not 100% efficient.
I agree that neither is 100% efficient.
Efficiency in this application is a a comparison of energy into the system to the work performed.
Efficiency of an automobile is concerned with moving the vehicle. The rejected heat is energy but we disregard it in our measurement because it is not the work we are trying to accomplish.
I guess a nuclear bomb efficiency should be measured by the destructive force, which can be heat, force and radiation. Interesting but not really relevant to the topic of the thread.