That the boat goes through pillars depends on the boat course is at the moment.
It also depends on the width of the river where the bridge is build.
The game uses 1x, 2x, 4x , and 8x long parts which the game connects together with a algorithm depending on the length of the total bridge which is drawn by the player.
It can happen because of the width of the river a 4x and a 2x are connected instead of a 8x and so you get a pillar between the two.
If that pillar is in the path of the boat it will go through it.
Boats can go through Tradeports and other buildings on the water too if the buildings are a few tiles into the water.
The boats path is set at # I believe, while for the Bannies # means they cannot go there, but sometimes they do anyway.
Just as Bannies cutting corners so go through walls at corners of buildings which are at the edge of game tiles.
Us modders learn more and more about the games sometimes weird behavior.
Years ago quite a few asked for the buildings to be placed on edges of the tiles so the roads would touch the edge of the building.
But because of that the bannies cut through the corners of the buildings.
If you look at Luke's buildings his walls are a bit inside the tiles so going through walls at corners happens less.
So it's a trade off, either live with bannies go through walls at corners which are at the edge of game tiles or the players have a bit of space between the walls and a road and bannies go through walls at corners happens less.
Cannot have it both.