Many board stuffing houses do that kind of thing, but company A that actually designed the board may stipulate that certain more expensive and often more precision parts are used. Company B may order essentially the same product but not be so concerned with using the higher quality parts to keep the costs down. The two epoxy PWB's are the same but the quality/tolerance of the parts loaded on it are not. I know for IC's there are often several performance grades available for the same product and there are also knock-off IC's that are not always the same quality either. Also, things like resistors can come in 10, 5,2, and 1% tolerances - some applications need a tight tolerance to be accurate and as you probably guessed, 1% can be a lot more expensive than 10%.
Same circuit board, looks the same to the eye, but quality parts can make a world of difference in quality and reliability.