Scantool does not make an ALL IN ONE obd-2 reader. Autotap does. If you buy the Scantool's tri combo reader, you'll get the cables, and 3 black boxes. You have to interchange the boxes to match the car's ptotocol.
From what I understand, Autotap's software only works with autotap. They do not offer source codes to you for writing your own interface. Scantool scanner will work with 3rd party software. I believe they even have to source codes for you to write your own software.
Both scanners seem to be able to clear check engine lights.