Seat stay "caps"

There is currently no way to specifically account for the shape of that seat stay cap. For now, my best suggestion would be to set dimension Z in the seat stay dialog box to locate the stays so the inner edge of the stay lines up with the outer edge of the seat tube. For simplicity, let's say the seat tube has a diameter of 30mm and the stays have a diameter of 16mm. I would set HF to 16mm and Z would be 30mm/2+16mm/2=23mm. The result would look like the image below.

With the new export to FreeCAD option, you could further refine the design in FreeCAD to better represent the end caps of the stays.