Here's what I personally do....
I never turn auto-recalculation on. I'd much rather find my own way back to my route as typically when I create a route in MRA I want to follow it exactly, and if I do have to deviate from it I want to decide how to get back on it.
If I want the gps to automatically calculate my route I prefer just to use Waze or Google Maps. That's fine most of the time in my car, but on the R1300GS or Spyder I almost always want the gps to follow my predetermined route.
As I mentioned I do use 1.2 .gpx format almost exclusively as it follows my intended route as it's forced to follow the track which is what I want.
I don't use Basecamp, Explore, etc. etc. or any of the other Garmin apps with the XT*. I find them to be unnecessary and frustrating. And yes.... I have spent many hours learning their strengths, weaknesses and quirks. I'd rather have direct control over downloading my routes and tracks to the XTs and deleting the old files out of the gpx folder when they're no longer necessary. For me, this method is very straightforward, foolproof and easy for me to understand.
If I'm sharing a route with a variety of other riders who may or may not have Garmin units that can properly import 1.2 files I simply share the track file. Virtually all gps units can create a route from a track that will follow the intended path.
The bottom line is for me what I see on my computer screen when I'm creating a route in MRA is what I expect to see and follow on my Garmin XT3, and the easiest way for me to accomplish that is to save the route in 1.2 .gpx format, manually transfer it to my gps and turn off automatic recalculation.
I always double check the distance of my route in MRA with what my Garmin shows after import and if they don't match VERY closely after import I investigate to see why they don't by showing both the track and route in the Garmin, then fix the issue in MRA and reimport the route.