I wouldn't be afraid to tour on a Cross Check. If you were going to go with panniers, I'd be more apt to choose the LHT, as the longer wheelbase will add stability and heel clearance. However, the Cross Check will be a better all-around, lighter handling, sporty bike, when you're not travelling. With the Cross Check, I'd look into a B.O.B. trailer for travelling.
Building up one with SRAM Apex compact crank, Apex mid-cage derailluer, and 12-36 cassette will get you a 25.8" low gear, running a 700X38 tire (common touring size).
XLAB and Profile Design offer a variety of alternative bottle mounts. So, I wouldn't let one less bottle mount sway me from the Cross Check.
700c wheels are definitely going to roll over rough surfaces faster. I've recently bought a 29er MTB and it's a considerably faster and smoother ride than my previous 26" MTB, even on pavement. If dirt or rock roads are going to be a regular part of your riding, as they are with me and my Specialized Tricross, then a 700c wheel makes sense. Since you're looking at building this bike, I'd consider a Peter White wheelset, as well.