Difference between Shadow register, match register and capture compare register in a timer module
Each timer module contains a free running timer.
The value of that timer can be read at any time by reading the value of the Shadow register.
Since the timer continuously runs, you have to monitor its value if you want to use it to generate a periodic event.
This could be done in software by continuously reading the value of the Shadow register, or in hardware by setting a value in the Capture/Compare register. Think of an alarm clock as a real world example.
The Capture/Compare register circuitry is also connected to hardware pins that allow the timing of external events, and also to allow the generation of external events in the form of  PWM output.
The Match register is used to set the desired intervals such as the PWM interval.
Look at section 1.3.4.4 on page 61.