No, it works. After two seasons, Arrieta can opt out... unless the Phillies believe he's worth the extension ($20 million/year, going up if he's not only effective but a workhorse for two season, or if he's a Cy Young candidate). So the Phillies control those out-years. Evidently no player options; MacPhail/Klentak make the decision, based on Arrieta's performance, and on whatever else they have available at the time. So they only extend Arrieta if he's pitched well, and if he's not in the way of younger options.
Arrieta gets $55 million over two years, plus a third-year guarantee of $20 million, insurance against declining performance. And if he's still effective and the Phils want to go younger (or don't want those last two years), he's in the market again.
Interestingly creative deal - a bit of a change for the Phillies organization.