The only real disadvantage of the traditional inboard bow stop is that it can be hard to get your cover on if you put the rub rail tight against the boards. To compensate for this many people don't put the boat all the way up which can affect how much it bounces around and what not.
I have the roller and I get it in the same spot every time when the bow eye hits the roller so that's not really an issue.
I could see where bow stops would give you more flexibility to put the trailer real deep in the water if necessary. If my trailer is too deep the rub rail will come up under the roller. If you weren't paying attention in that scenario you could damage it. If I need to load deep due to a particular launch I have to get the boat all most all the way onto the trailer then pull out to normal depth and pull it up the rest of the way.