Well testing on the live map, with destinations just short and right after where your proposed route and waze's route merge, shows that the routing server can go that way. So apparently no map issues causing this.
So most likely this is what is called route pruning. As the distances get larger, the more options are available to be used. Because you want a route in a reasonable time, the routing server has to take shortcuts to try and limit the number of options to evaluate.
One of these is preferring higher grade roads over lower ones, which is why I think that the first suggestion is the longer route. If you slowly move the destination further and further out, you will see that the 2nd alternative given keeps being your proposed route, till it reaches 100 miles, then it stop suggesting it. So it appears that based on some behind the scenes pruning rules, it stops investigating this alternative at 100 miles, even though in the long run, it will be better.
This is one of those that you will need to take to support via the nanorep section of the support webpage, as unfortunately it's not a simple map issue.