Mercurymoto67, are you asking the difference between cafe and flat tracker or cafe and board tracker? Both "trackers", two totally different style bikes. First thing that came to my mind was board tracker, hence the fifty years answer I gave.
I think the bikes I posted are more cafe than flat tracker, Mostly due to the seat/tail sections. Besides the first bike I posted, none really have fairings or clip on bars as traditional cafes. But they are in the same vein.
Cafe-ish. Low stance for lowered center of gravity for better handling. Clip ons. Hopped up fast engine. Most of the ones I posted are more in this vein even though they don't all have clip ons, they all have low bars. Japan's version of a traditional sportster cafe.
Typical flat tracker. XR750. Notice aggressive dirt tires. HIGH stance. Exhaust is VERY HIGH, almost at tank/seat pan level. The fact that it has a seat pan is about the only thing it shares with a cafe.
Board tracker loos like a very old anitque. No real explanation needed, self explanitory, you know one when you see one. This is a nouveau example. Totally awesome. Totally Japan.