I've had both, and tried to race both (when I was learning, I tried to race an XR600 - stupid decision, as I'm only 170cm tall, and was 68kg at the time)
I did a 20,000km Half-lap of Australia on my XR600 - fantastic bike for the trip; used a bolt-on Acerbis tank, and didn't have any issues, apart from a camchain issue.
Anyhow - I bought an XR400 back in 1997 that was modded for racing enduros, and that bike smoked XR600's on bitumen in straight-line drags, and felt MUCH better and lighter to ride than the XR600, as some of the guys were quite interested in the "little" bike that smoked them in the drags, including roll-ons.
Saying all that, it was running a JE hi-comp piston and a mikuni, so for long distance riding you wouldn't go for this option - I merely mentioned it to illustrate that the XR400 has some capability.
So -after selling the XR400, and owning some other bikes, my riding style changed, and I now have an XR400, 2005 model which I have kept stock, mechanically; to maintain the reliability, but I have spent a lot of money trying to sort out the suspension. One thing to note ther - it's
NOT a KTM-equivalent, but I bought it for my purposes.
I've done a couple of good trips (1000km+) shake-down rides on the bikes, and am very happy with it as an all-rounder. It feels lighter than the XR600 due to reduced engine braking, which makes it alltogether easier to ride for longer periods, which is a good thing, in my opinion.
As to luggage, I normally carry a backpack, and a water-proof duffle-bag for the camping gear.
bike upgrade details here:
Garage Upgrade - ADVrider
Out trailriding:
desert trip here:
Golden Quest Trail - ADVrider