Of course flanging it is easier. So is slathering the quarter in fiberglass and bondo instead of doing all the metalwork to get it straight. That doesn't make it the right way to do it.
If you flange it because that's the easier way to do it, that's fine. Not everyone has the skill to do the repair with the proper method, and that's ok. Butt welding a panel like that is difficult, it's easy to warp the panel. Flanging it takes less skill and that will ultimately mean less bodywork for someone that doesn't have the skill to do the butt weld without warping the quarter. But if you flange it, don't go through the extra trouble of then covering it up so you can pass the car off as something it isn't. Just leave it the flange seam- that's the way you did it. It's not the best way, but it's ok. There's a seam there, and the next guy will know that's how the repair was done and can make a decision from there. There's nothing wrong with that, if you flanged it and did a good job the repair will still hold up for a long time.
I mean seriously, why hide the seam? It's on the backside of the quarter panel in the trunk. You don't see that at a car show. You don't see that at all unless you're looking for it. The only reason to go through any extra trouble to hide the seam is to hide the fact that the repair was done that way. Which means you already know it wasn't the correct way to do the repair, and you're trying to hide that fact from someone else. Maybe the next buyer? If you do the repair the way it's supposed to be done, there's nothing to hide. If you flange it that's fine, but don't hide it so you can pass the car off as a higher quality build than it really is.
Disagree if you want, but there's a reason why restoration shops insist on using butt weld on panel replacements like this. It's the best way to do it, and it's the right way to do it. It's also probably the hardest way to do it, but that's life.