You can get much closer to your subject with a lens designed as a macro lens. In your example #1, the 100 mm f/2 EF lens can only focus on subjects >3 ft away from the imaging sensor. In contrast the 100 mm f/2.8 Macro lens can get as close as one foot from the imaging sensor to the subject and achieve focus. This means the front of the lens is within about six inches of the subject. The distance to the front of the lens is often referred to as the working distance. The distance to the image sensor is what is measured for the minimum focus distance.
This gives the Macro lens a higher magnification power. In this case, it has a 1x magnification, which means that if you get close enough to the subject, the image on the sensor is the same size as the subject itself. Good for photographing bugs and small flowers and such