Hi arjun,
The set_clock_latency with early/late can be used for jitter margining (as shown in the doc you attached) , but I would keep this command for clock tree variations only as roli mentioned. The reason is that when you move from ideal to propagated clocks, this command goes away and you will need to account for jitter some other way. It's best to keep it consistant both pre and post CTS.
The set_clock_uncertainty will be applied the same both pre and post CTS. One issue with using this to apply jitter is that multi-cycle paths will not be accounted for properly. Say your frequency jitter can speed up your clock by 100ps, and you are timing a multi-cycle path of 4, set_clock_uncertainty will only give you 100ps of margin when you really need 400ps.
Another way to account for frequency jitter is increase your clock frequency. This fixes the multi-cycle path problem as the margin added would then the correct 400ps.
The increase frequency method works for frequency jitter but does not account for 1/2 cycle jitter. If your design has a lot of 1/2 cycle paths you can also use set_clock_uncertainty with rise/fall options to account for 1/2 cycle jitter.