Work is work and a kJ is a kJ, but that doesn't mean that 1 kJ equals exactly 1kcal for everybody. "kj work equals calories burned" is just an estimate; it's a pretty good estimate, and better than anything other measurement short of a gas exchange mask in a lab, but it's not an absolute truth.
What you say ^ is completely true. But, again, the difference between any two humans on road bikes is going to be within 5 %.
I guess it gets to be a question of what do you need to know for? Calories burnt isn't a useful metric for training, it's really a diet question. Assuming 1 kJ = 1 kCal isn't perfect, but we're talking a maximum error of a single oreo every 30 miles.