Also that Phelps thing is highly questionable. He says he "probably" burns 8-10k, not 12k. Not the type of statement you want to rely on to dismiss all this work.
Clearly there are some details that matter here...
I'm pretty sure this doesn't apply to extreme cases like modern athletes, who explicitly push their bodies in many ways that normal fit people don't, and who have teams of doctors and coaches that can force them to keep up with exercise and diet even when their bodies are telling them to stop.
Maybe I should bring it up with a doctor, but I feel fine, I just also spend more on food than most.
BTW there are diseases that reduce calories absorbed, you might want to get checked for colitis ulcerosa and crohn's disease. They have nasty side effects so better to know earlier even if you don't have the worst symptoms.