The thickness of thread varies, naturally, and that thickness affects embroidery in terms of needle requirement and coverage. The program does make use of thread weight for a few bits of automatic process: particularly short-stitching which happens when a satin stitch turns very tightly.
The program assumes normal weights of thread unless you tell it otherwise. You can do this by naming any threads with a weight, ex: Somethread 12wt. The program will notice the label of the thread and adjust things like short-stitching automatically.
For a more in-depth explanation of thread weight, refer to the Color section of this manual.