That guy is wrong. Even though the exact numbers won't always be the same every time Oda draws it, the math is legitimate and is nothing more than conversion problems. I do it all the time in chemistry, albeit the concept is different, the underlying principle is the same. I've also done it in history classes with maps, which also aren't always done the same, and in geometry. The math is and principle he used is sound. While the scale may not be identical every time Oda draws it, nor may he have the scale in mind, it holds up and is still there. That's why it's a rough estimation and not precise.
I'm almost certain that most artists try to keep up consistency in their drawings
We've seen Oda have some incredible consistency in MF so while he may not make the exact number of pixels each time or break out his ruler, he'll still try to draw things in similar enough placement because that's what artists do. You're making the confusion that Oda drew it with the intention of it being 6 KM in mind, but that is not so. Oda didn't draw it that way with the intention of it being calculated to 6 KM, that's just the number you get if you so happen to choose to do the calculations.
I got the scale mixed up though, Green Bit is about 6 KM from Dresrosa not several hundred KM. Still, to cross that distance in a second or two is still great speed.