I think the geography and history of the region is playing a part here. These castles are at chokepoints, it's just that they are water chokepoints. Eilean Donan sits at the narrowest point between the sea and two large lochs, and because the highlands are basically nothing but hills and lochs the easiest way to get around there for most of history was by boat. I'm less familiar with Ardvreck, but it looks like the waterways are navigable from the sea up to the point of the castle, and the castle controls the best place to embark or disembark.
Additionally, most of these castles were for handling other highland clans and conflicts between the lowland-based government and the highland clans. They weren't trying to stop the full weight of a massed French invasion. On that smaller scale, there's less likelihood that someone will be willing to properly siege you out and even less likelihood that they can do so when you can just take a boat to the other side of the loch.