Thanks for all the input, folks.
Fenders: I would like some, but it's not the highest priority. Once I get the bike rideable and put some miles on it, I'll decide then what (if anything) to do about fitting some kind of fender. Probably raceblades or nothing.
The dropouts are adjustable with 8mm fore-aft movement. Should work just fine for this setup.
IGH: I bought the wrong one, although in my defense the right one won't be available from anyplace until late spring or early summer.
I got so excited to find an X-RF5 in stock somewhere that I didn't realize that it's not the X-RF5(W) that I want until it was pointed out by member Dan Burkhart when he saw the pic in this thread. The plan was to use the Sturmey Archer bar-end shifter, which requires the (W) hub. Ugh. I feel a bit sick. Seems like the wait for (W) hubs is months long at this point, so I'm going to use the hub that I have in hand and use the twist grip shifter via a hubbub adapter, even though it's ugly.
I've test fit the Velocity Deep V's from my other bike, and I like the look, and there's definitely room for a 25 on there, which is what I plan to use (probably Schwalbe Marathons). I suspect that even a 28 would work just fine. I have put thousands of city and touring miles on 23's and have no concerns about the comfort factor of 23-25's.
As far as the spacing is concerned, right now it's at 125mm, and the hub is very close to 115mm wide. I'm going to leave it up to my builder to decide whether to use spacers, cold set the frame, or both.