Imperfect stud alignment is a non-issue for canti brakes (within reason). The critical issue is brake shoe to rim parallelism, and as long as the studs are close to inline, you'll adjust the shoes the same way as you normally do. The only time stud positioning becomes critical, is if you're mounting something that connects both like a brake booster. Of course, with imperfect stud placement, you'll have no choice about using shoes with a float system like convex/concave washers.