A lot of "29er" and 650b wheel-sets have mtb, or Boost spacing, because they're "mtb" sizes. 700c is the exact same size as the "29er" BS, but without the stupid marketing term. But to answer your question, a lot of your trouble is being in the US or perhaps high population western Europe, where marketing the latest crap is king. You'll find 700c rims and 135/100mm hubs most anywhere but third world countries. You'll likely even find limited supply of cheap ones there, and some tires that probably won't be suitable for your needs(but may get you by). A lot of the reason you see a few different newer mtb "standard" hubs is because they keep changing it, so people have to keep selling their nice wheel-set when they get a new bike every few years. If you're just touring in the US or western Europe, go ahead and get one of the new "standards." You'll probably be able to find parts without too much difficulty if something fails. If you plan to leave the US, I'd recommend skipping the new stuff and sticking to 700c(29er if you must), or better yet, 26" wheels with standard 135/100mm hubs.
Rim breaks are also probably a safer choice for touring in very poor countries. I have seen cable disk breaks in larger populated areas in Central America, and you'll find them in Asia since they make all of the bike parts there, but they might not be as common everywhere. Personally, I've used cable disk breaks for thousands of miles(likely tens of thousands but I don't keep track) without a single issue, and a spare set of break pads is tiny and doesn't take much room. I'm comfortable touring on them basically anywhere. I would avoid the new "flat mount" disks and stick to ISO or post mount. As for whether using standard 135/100mm wheels has saved me, no, because I'm not very heavy, pack light, and ride light. I've never had a wheel problem on tour. I've been places where modern hubs would have ruined a tour if I had a problem.
If a bike shop is so specialized that they can't easily, and knowledgeably set you up a triple crank drive-train, go to another shop. That's in the mechanics 101 class, and they must have skipped some chapters of the basics...
Nice frame. Congratulations. I'm sure you'll love it.