I noticed something interesting regarding Option 5.
It not only freezes the timer, it also freezes NPC movement.
So option 5 is not only useful for timed missions like kill X soldiers in 1 minute but also for missions like prevent Enemy Boss from escaping/enter base or prevent Enemies from rendezvousing.
Once you activate the cheat, NPC generals will basically wander around in more or less the same spot on the map while your character can hunt him down. NPC characters will stay in the same area of the map but they will continue to fight enemies in sight, so it is possible that fighting NPCs gradually move away from an area in pursuit.
Note: the NPC freeze applies to your secondary character as well. So if you issue a command to your secondary character to hunt down the enemy general for you, your secondary character will also act like he is lost unless you switch characters.
I was planning to post this as well. I know I came far too late to post it, 2 years later. I can confirm this as well. Only use the timer freeze if you are dangerously close to the remaining of 10 secs.
Also this option can preventing to complete the objectives (mainly bonus objectives) because some objective have conditions such as specific npc will show up but it preventing the objective for specific npc to activate.