On the question of GPX error - there appear to be system limits in the underlying technology that create issues for very long routes. The simple approach is to split the route and "link" them in mycycletour. That means you end up with more than one file to load, but that's not such a bad thing for GPS devices. You can certainly store multiple days in a single file (at least in my experience).

On the topic of bike friendly roads - the routes are planned using google which looks for specifically for bike routes, and if it doesn't find any then goes on secondary roads. It shouldn't be taking you on dirt / gravel roads. I've this problem when having my garmin gps set the route - i.e. you end end up on a dirt path over a hill... or worse. At least with MCT you can do the satellite view and take a look at the road.

On the campsite question you can now see campsites and other accommodation on the map when you go to displayroute. Once you have your route planned you can pick your stayover points by going to the map - just above it there's a pull down called "Places" and you can select "campsites" or hotels, or coffee, or pizza, etc.