sim:tests: Fix shodan robot test script

Add following cleanup
 * Grab the bundle ID at the runtime for ML execution.
 * Add the virtual timestamp at SMC UART so we can check the virtual
   time differences between commands. This is only for the robot test,
   while `m simulate` as a cleaner log
 * Add comments to make each steps of the test more clear.

Change-Id: I9fd0eb942d593c195fa574ada1824550a2fae350