Using four year splits is pretty misleading as it includes his complete outlier of a season that he's never come close to duplicating since, while also including Upton's ATL numbers which are his worst by far and not reflective of what he's done the past two years.
Over the past three years, Smoak has a 97 wRC+ against rhp, for example. He's essentially had one good season against rhp in his entire career (2013 where he had a 138 wRC+ against them). Outside of that he's either been average or absolute s*** against them, and that's on top of being a lumbering, slow-footed, below average first basemen. Even if you want to say he's about ~100 wRC+ against rhp, is that worth taking one of your better hitters who can't throw due to injury and is an injury risk to begin with and sticking him in a more demanding OF position where he's probably going to be below average defensively? Pearce is already an above average first baseman on defence. Upton is probably above average on defence in left (he was very good there last season). Even with Upton's struggles against rhp, is the difference between those two lineups significant enough to warrant putting Pearce in the outfield? If they want to put Morales at first and DH Jose, then sure, stick Pearce in left. But to do that to get Smoak's bat in the lineup? Not worth it.
If you asked me who has the higher WAR next season, I think Upton beats Smoak if both are given equal playing time.