The errors either cancel out (if error in both directions) or they work in one direction ("bad" foods like junk systematically underestimate calories, "good" foods like protein powder systematically overestimate calories).

Either way, if you count calories and compare to your weight gain/loss over a few weeks and adjust your calorie target as warranted, assuming the types of food you are eating do not change drastically (e.g. you calibrated on regular diet and now have started an elimination diet), the error bars can be basically ignored.

Exactly! My point was that despite the precision of calories we should really think of them as ballpark estimates .