not always, it depends on the bargaining power of the involved parties
Imagine this scenario: a club from an average league wins promotion to the Champions League. they have a important player which they want to keep due to European games. the player has a few months left on his current contract. if any club bids for him, he could leave but he may also think that playing for that club in the European competition would promote him and allow him to leave for the better club. so what he does is that he signs a big contract with a relatively small buy-out clause to when his team gets knocked-out from Europe he can leave the club whenever he wants (providing that anybody wants him). If he stays he's left with a big contract. This happened a few times in Poland you know.
Now, how this could apply to Rooney.
Fergie made it clear that for some reason he wanted to keep Rooney. Rooney might have actually wanted to leave but he figured it out that announcing that during the Rooney-gate would left him play either in reserves or watching games from the stands. he also was cup-tied at that time so his negotiations position would be weaker.
Fergie didn't want to unsettled the team during the season so he offers Rooney a big contract. Rooney doesn't know if he is going to stay or not nor did he want to leave during the season so despite getting a big contract he includes the buy-out clause so he is independent from United's will. Imo he had all the cards during these autumn negotiations.
to sum it up: United are left with world-class striker at least until the end of the season and will recoup at least 25 mil should Rooney leave. Rooney gets a big contract with a relatively small buy-out clause. Win -win.
I wouldn't rule out the existence of 25 mil buy out clause
Edit: imo this vey low 25 mil buy-out would justify the 200 k per week contract. these insane amount of money is a counterweight so Rooney doesn't leave to early or there are only few bidders ready offer him similar terms. i bet Rooney knows that.