If we take two athletes one (A) have FTP 200 and another (B) FTP 250 and ask them to do same excersise, let's say 500 kJ/hour, obviously A will have higher TSS for that exercise and his average heartbeat will be higher.
Doesn't he supposed to use more calories that athlete B producing same 500 kJ/hour? If so for how much more? How to calculate that?
As mentioned above, the conversion factor from kJ/hour to calories varies from person to person, but it does not vary much (the variation is about 5-10%) and it does not correlate with FTP. (The biggest residual is actually cadence. All else equal, you burn about 60 more calories per hour pedaling at 100 rpm than when pedaling at 60 rpm.)
If you're looking at this from the weight loss point of view, if you shoot for a 1000 calorie/day deficit with 500 calories from exercise and 500 calories from diet, the uncertainty in power meter based deficit is about 50 calories - basically insignificant.
(This all applies to exercise below lactate threshold. Once you go above lactate threshold, things get more complicated.)