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All City is spaced 135 at the rear, so Alfine will fit.
Quick read of the website says it has internal cable routing, but not sure whether that means you can run a cable to a hub gear, you may want to have a chat with @HoKe, as he's got one, though he runs it single speed. I'd assume it does otherwise why the 135 spacing so you can fit a hub gear?
Di2 might be an issue, in terms of where you put the battery for it. I've only looked at full builds with Di2, so haven't thought about what I'd need to do if I just built up a Di2 alfine wheelset solo.
Considering fitting my http://allcitycycles.com/bikes/nature_boy_disc
With a hub gear, anyone got any advice? obviously theres no cabling for gears but DI2 might be an option, alongside the rear disc cable?