The only "justification" I can think of (excuse?) is that, once properly reamed and faced, you are dealing with bare metal. Left unprotected by the grease and the headset getting jammed in there, then you've got a corrosion problem. I think there's some validity to that. Of course there are work arounds by shipping in some grease, etc.
I'm OK with Surly's concept of we face it before we paint it, just razor off the overspray. It worked on one of the two bikes I've seen built. Not exactly a valid sample, nor am I speaking from any great depth of experience and knowledge.
I'll also admit that the skinniness of the steel head tube on the cross-check, compared to the two beefy MTB aluminum frames that I built up in the past, really had me on my heels. I was tempted to NOT have it reamed just because it didn't look like there was anything to it.
Oh well, that's why I'm building the bike instead of buying it -- to have a little fun, and learn some.