The period that you're referring to was one in which the highlands of Scotland were to a large degree independent of control from Edinburgh, on a day to day basis at least. But that does not mean there was no need for defensive structures such as castles. This was a period of significant conflict between highland clans, one characterised by raids on rivals' territories to exact vengeance for earlier incidents, seize cattle or destroy crops. Such raids were often carried out by sea, using shallow draft galleys capable of navigating even quite restricted waters - the Lords of the Isles, based in the Hebrides, were one of the major regional powers for the whole of the period up to 1493, controlling about 5,000 islands and 25,000 square miles of territory, and their power was almost entirely based on their command of the seas.

So while fortified residences such as Castle Stalker were indeed used in time of peace as ways of displaying a clan chief's wealth and status, they also served as vital hiding places and rallying points in time of war. Mounting canon, and indeed resisting a siege by a force equipped with canon, were not significant problems in this period, since gunpowder warfare made its appearance relatively late in this distant corner of the world. But being able to keep your men, women, children and indeed livestock safe from a short, violent raid from the sea was a very important consideration throughout.

So castles like Stalker are not uncommon in the highlands, and several are placed in very similar positions - at the heads of sea lochs that offer access to the interior for forces arriving from the isles. A personal favourite is Castle Tioram, on Loch Moidart, although Eilean Donan castle, on Loch Duich, is probably the most famous and most picturesque of all.

The consequences of lacking a safe redoubt in this period can be illustrated by one of the most violent incidents in all clan history, the raid on Clan Macdonald and the island of Eigg by the rival Clan MacLeod in 1577.

The group were desperate for revenge after its clansmen had been castrated by the MacDonalds for making unwanted advances towards the ladies of the island.

The terrified MacDonalds caught wind of the MacLeods plan and quickly rounded up all the island’s residents, seeking refuge in the gloomy St Francis Cave. The cave’s entrance was hidden well and cramped, only allowing for people to enter a few at a time.

The secretive hideout at first seemed to have done its job, as disappointed MacLeods, unable to find anyone in the island, began to depart. Unfortunately a careless lookout gave away the location of the cave at the last minute. The tight opening of the cave, that had made it so hard to find, was also to be the clan’s downfall as the same constricted cave mouth stopped anyone from escaping.

The MacLeods were able to cover the cave mouth with straw and lit it on fire. As the cave filled quickly with thick smoke, all the people inside were suffocated. Only one family on the island managed to escaped the massacre because they had taken refuge in a different cave.

The number of how many died is fiercely debated, with between 200 and 400 souls believed to have lost their lives.

Source

Andrew MacDonald, The Kingdom of the Isles: Scotland's Western Seaboard c.1100-1336