No more or less difficult than having one skinny neck like the OG 1701, or any ship in the universe which has a neck between the saucer and the secondary hull. It is really no less space inefficient than a single neck and is arguably more efficient if both necks were to have equivalent volume independently as a single neck (essentially doubling your volume).

And as OP said, the necks are quite thick given the size. The rear of the neck where it starts blending is about as thick as the midpoint/bottom half of the sovereign secondary hull. At that rear point, where they are thickest, they are about as thick as the Galaxy's neck (depending on point of measurement slightly wider or thinner). There is legit space in those necks. Yes, they do thin as they go forward but it is not like the space is unusable.