Is the 27 wRC+ swing between Smoak, being above league average vs RHP, and Upton being basically Pillar vs RHP offset by Bautista's D that much? It's not like you can't pull Bautista in the 7th/8th if you have a lead and need better D, let him get his 3 at bats.
Who knows what's bothering Travis, might have a cold, might've slept funny and has a cramped neck. I'd prefer to give our manager the benefit of the doubt until we hear more.