You could start with a frame and build it out with a parts package. The same shop selling the Salsa may be able to get it as a frame, with a discounted group package more to your spec. A Surly LHT disc, same thing -- you could have a shop build out the frame; same distributor they order the frame from has group package deals which allow for some reasonable customization. The Disc Trucker complete is $1400 msrp, which gives you $100-400 budget for upgrades and add-ons -- the only thing it doesn't have which you're looking for is a compact crank.

Soma also has a CX bike, disc compatible, which should build out to not much more than the other bike's you're looking at.

If you're talking to a shop about a bike purchase, they should be willing to work with you on upgrades, like discount + free install on upgrade parts, or instead of discounting new parts, shop cost for take-off parts in trade against the upgrades.