I suspect your issue may be caused by the following:
Because some of the smaller faces weld to the edges of the larger rectangles it creates additional edge vertexes. The SU geometry engine then no longer sees the large faces as rectangles (4 vertexes) but as multi-vertex polygons which requires a less efficient triangulation of triangles with collinear edges. It would add a lot of overhead for the algorithm to check if a multi-vertex (more than 4) polygon has the shape of a rectangle prior to to calculating triangulation so it employs a generic triangulation for a polygon with any number of sides and of any shape.
You could possibly solve the problem by creating a ruby processor that will iterate through the planar face entities and checks for collinear edges in polygons with more than 4 vertexes. If such a condition is found the processor should create a new face inside a group (to avoid welding with other edges), with only the vertexes that define the shape, (eliminate all collinear vertexes) and then delete the original multi-vertex face.
Theoretically this should solve your problem as the SU exporter will then triangulate between only the desired vertexes.