I mean, expecially for games like final fantasy, are we suppose to do some breaks? And if yes how do we calculate the time?

Typically you'll need to leave the timer running, but yes, that's a game by game decision. Some games might allow exceptions.

If you go AFK and leave the timer running, yes. If you stop the timer and do the run in multiple sessions, then that's generally not allowed in RTA and makes the run Segmented. These sorts of things are often reviewed on a game-by-game basis though, so as the previous posts say, consult your game's mods for rule clarification.