Our mitochondria process the total of our energy needs every day, while exercise adds, percentagewise, only fractional additional energy need.
do you think mitochondria notice the difference? I don't.
If I cut my caloric intake, I drop weight like nobody's business, and that's all thanks to my mitochondria at their place in the chain. It's the same thing my mitochondria are doing when I overeat and put on weight.
If you live paycheck to paycheck and then get a 25% salary increase, if everything else stays the same, in a year you have already saved 300% worth of your original salary vs 0%.
That is even with your unwarranted assumption that all energy use is the same and doesn't cause different adaptations. This kind of simplicity is just not happening in biology.