Currently, BikeCAD only works out the miters at the end of the tube, not part way along the tube should it happen to intersect anything else along the way. It could be a little tricky, but you could create a second model that has the stays ending at the seat tube and obtain your second miter template that way. This second miter template would only have the back part of the template as another assumption that BikeCAD makes is that when our seat stay is mitered to the seat tube, no part of the stay extends beyond the centerline of the seat tube. In your case, that's not so.