I don't agree. The opt-out is something the player wants, not something that the club needs. It's insurance against a sudden end to income. If the Phillies are willing to spend $xxx on an Arrieta contract, and really only want/need his services for three years - well, giving him an opt-out at the end of three years, with reduced salaries after that if he doesn't opt out, costs the club nothing if the total over five years is still $xxx. At the same time, it gives the player the possibility of opting out, and increasing his salary in years four and five by negotiating a new contract (with the Phils or somebody else), if he's still effective.
Now, I agree that he's not all that likely to be very attractive in the open market in years four and five. But he may not believe that. In fact, given that he's an elite professional athlete, the likelihood that he's rational about his own inevitable decline... well, it's not a high percentage. So the opt-out is likely to be attractive to him. And if it's at no cost to the club...what the heck. Make him happy.
Yes, they could sign him for three years, for the same total money - and if he got the money sooner, he'd actually be ahead, assuming any reasonable investment strategy. But that's pure economics, pure rational analysis. People don't run on pure economics or rationalism. Many players, for whatever reason, appear to want the longer contract, even if the total money is the same. Clubs may also want it - if only to appear not to be "overpaying" in a given year. (Remember the hullabaloo about "overpaying" Pat Burrell in the last years of his contract - although the annual average of that contract was a steal for the Phillies?) Again, this isn't about pure rationality; in this case, it's about PR appearances.
So there are reasons why both the player and the club might want to spread a given amount of total compensation over more than three years. If they do... well, that's what "negotiations" are about - about finding out what both parties want/need, and trying to find common ground. And... what we want - what fans in general, or a given fan in particular, want - should be irrelevant. If it works for the front office and for the player, then it works.