I presume that last night's lineup is the "real" lineup with a little bit of shuffling in the bottom half once Hoerner is back (Hoerner 5th, Shaw 9th?). Counsell is clearly following the Braves/Dodgers playbook of maxing out the power at the top of the order, and I'm here for it.
So I think you're right about how a guy like PCA, whose OBP is going to teeter on the edge of the 2's and 3's, shouldn't actually lead off. I also think that for the Cubs lineup specifically, you *want* him down there at like 7th.
Unless Dansby can get his groundball rate back under 40% or Gage Workman is starting on a given day, there's not a plus power hitter in the 5-9 spots of the Cubs order. So I want Nico and especially PCA to run like hell. The proverbial three run bomb likely isn't coming until the lineup flips back around to Happ. So A) you need to pull the other levers you have to pressure the opposing pitcher and B) the opportunity cost on a caught stealing is comparatively low.