RTC = Real Time Clock
The 3DS stores two different time values. Time starts after inserting a battery. Setting date/time in System Settings just changes an offset, not the actual internal time.
This way games like Pokemon can prevent the player from cheating in time based events by adjusting the clock. The game stores the real value in its save so System Settings has no impact (or if it stores both values even enables the game to "punish" the player for attempting cheating). For the same reason you should not insert a Pokemon cart in different consoles (with different offsets). It might silently trip a cheat protection and reset time based events.
GodMode9 can modify the real time (and enable cheating time gates this way). Setting the offset to zero is just for not confusing the user. If you set the correct time/date in GodMode9 without having the offset "0" and reboot, Home Menu will show garbage values (most likely far in the future).
There is no technical need to set the offset to zero.