Usually if an area is unused in the MSQ it is used in at least 1 sidequest or class/job/role quest.

That area of Mor Dhona I recall being used in the Summoner quests. I don't really remember to what extent that area of Coerthas was used. I don't remember ever visiting that area of the Dravanian Forelands, but it has been almost 10 years...

In any case, they have been using places like that for variant dungeons so it could happen eventually.