The mid-bore dual-sports are nicer in the dirt, but you've got to work them harder on the highway to keep up with traffic. That tends to kill your mileage quest. Heck, I've had to keep an XR650L pinned a few times while going uphill into a headwind, with a resulting loss (almost alarmingly so) of mileage.
I spent six days in Baja two years ago on a 625 SXC. KTM introduced it at that time to compete with the niche that the XR650R fills nicely, with the added features of electric starting (big plus), suspension tuned for the more aggressive rider out of the box and the legacy of KTM's factory Dakar Rallye racers. In the dirt, it's great compared to the other bikes you mentioned, but that's because it wasn't really designed to be a street-legal bike in this country. You can get away with it, but it's just not going to be quite as smooth on the street as the dual-sport bikes from Japan, simply because those things were designed for what their marketing research showed: The guys who bought their bikes tended to ride them on the street (back and forth to work/school, errands, etc.) 80 percent of the time. Hence, the emphasis on streetability.
That said, converting something like an XR650R to license-legal status (as opposed to just buying an XR650L) results in something more akin to the KTM. It was designed as a dirt bike so it won't be quite as comfortable and smooth on the street, more so on longer rides. It will, however, be superior in the dirt to the bikes that were designed in the first place as dual-sports with the emphasis on street.
You've got to truthfully (to the best of your ability) answer the question of how much street and how much dirt use do you likely forsee? If you wanted the nimblest all-around machine, then the DR-Z400S is pretty good; just be aware that it won't match the bigger bikes on long, fast road rides, especially when loaded down and heading uphill.
If you're interested in the best dirt performance in a big-bore, KTM hands-down. Just don't expect it to be quite as comfortable and smooth on long road rides. Don't worry about reliability; the LC4 engine is what they base the factory Dakar Rallye racers on, and those things are next to bullet-proof.
Of the three big-bore Japanese machines, IMHO the Honda 650L is by far the best if you're most concerned with dirt-worthiness. It's tall, but you can pound whoops pretty darn fast as long as you keep it straight (ride the rear brake lightly and keep the thing pinned).
The Suzuki is an oft-overlooked sleeper. It probably strikes the best compromise of the compromise bikes in that it's not quite as good in the dirt as the Honda, but I think it's better there than the Kawasaki.
Ah yes, the KLR650. Best bike if you're into long-distance riding. Definitely not dirt-oriented, though you can certainly ride it on trails better than a 2002 BMW GS. My complain about it (besides its overall girthiness) is that the fork flexes way too much, and the front brake is way too weak. Both are byproducts of the bike's age; these things were fairly contemporary (though not really state of the art) when they were introduced 15 or 20 years ago. Kawasaki hasn't changed them significantly (beyond Bold New Graphics) since.
If you can, beg or borrow rides on each to see which you like best. Then, buy it and have fun!
ETA: I had an XR650L as a long-term test bike for a little over a year, and it averaged around 70-75 miles before I had to flip it to reserve when ridden primarily as a commuter bike.