Can you show me a before and after screenshot?

Right. So here is a map with six tiles on a base tileset:

The dirt patch on the left has a rectangle object, the white circle, a collider body, is hanging on this. Next to the dirt patch is a brown "hole" with an ellipse object inside. On the upper right is an object layer polygon that is also collidable, which is automatically drawn by Box2D itself. The four evenly spaced tiles on the middle contain polygons that trace the non-grass parts of it.

This is the same thing but calling box2d_draw on the map:

The collision shapes are defined correctly for the ellipse and the rectangle, but not for the polygons. The top left contains some weird polygons that aren't supposed to be there. The polygons are defined on the four right-most tiles like this:

After applying the fix, the polygons are correctly placed upon the tiles:

The root cause, as it appeared to me, was that tile object ellipses and rectangles are drawn by the dx and dy coordinates of the tile objects, which are automatically calculated first here and then here. Later, o.x and o.y are used to draw the rectangle and ellipse tile objects.

On the other hand, the polygon inside a tile object is not drawn based on these coordinates, but is based on the vertices of the polygon itself directly, not the dx or dy values. While the dx and dy are correctly calculated for the polygon itself but not for the polygon vertices.

Going deeper, we find that for object layer polygons the vertex coordinates are adjusted during load here. This same calculation — or any calculation — is not applied to the tile objects. This is fine for rectangles and ellipses since those do not need recalculation, but for polygons this is necessary, since they retain the original "offset' coordinates of the tile object.

Awesome, thanks for catching this. :)