It's also important to realize that a six-year contract means that the actor is committed to the show for six years, not that the show is committed to the actor. So they can kill him off at any time.
And they may well plan to kill him after Season 3 (random example), but still give him the standard six-year contract, because who knows what will happen? Maybe he character will become super-popular, or maybe the actor who was supposed to take over as lead in Season 4 dies, or whatever. It costs the studio nothing to lock down the actor, and gives them options that they m not have if the contract is tied to the length they originally planned the character to be around.
Now, I'm not saying Tyrion dies or lives for any length of time. I'm just saying that contract is a business deal that is not necessarily tied to the writers' specific plans.
“I wish I had my knives.”
“You won't need them.”
“I never need them.”