It comes down to what we reasonably expect from different companies and what we are willing to pay. If you want cars that capture the general look of the Daylight but forgo the more expensive little intricacies, you go Lionel or MTH and save money. When you want the best of the best, you look to brass importers like Weaver and GGD and pay more for ultra-correctness.
In the case of flush windows, ALL companies need to get this right, as it is a most basic of details. So yes, unfortunately I have to dismiss the Lionel cars from my consideration. I'm paying for models that are pleasant to my eyes, not for those bulging green windows to stare me in the face every day