I'm not Malcolm, and I'd be interested in his response as well, but here are a few thoughts on the topic.
If you have received HYT empowerment then you have Samayas....there's lots that can be said about Samayas, but the main thing is that you must guard your pledges and maintain them to the best of your ability. In every manual that I've ever read, it is always stressed that first one gains the empowerment, then one practices, while maintaining one's samayas. Without guarding the samayas, there is no accomplishment. Samayas are perhaps more important than the actual practice sadhana itself.
There are samayas that concern view, and samayas that concern action or activity. In addition, there may be samayas regarding the practice or recitation requirements. For many protector propitiations, it is required that one offer torma, for instance, on a daily basis. That's a samaya. Without the Jenang, Jinlab, or Wang of a give practice, though, there is no requirement. So that's one aspect of samaya regarding protectors.
Another aspect is that Protectors activity is to guard our samayas. Some people think protectors are there to "banish outer obstacles" on the path. That's partly true, really....but more importantly, the obstacles we create ourselves, through misguided actions, are the biggest problems. So, protectors can manifest in our experience to remind us, or help us, to keep our samayas. In this sense, they protect us from ourselves. This is another aspect of the relation of protectors and samaya.
Malcolm said that, for those without empowerments, the 3 Jewels are our protectors. If you contemplate how this can be, and think about Protectors,empowerment and associated samaya, and how the Inner Path of Tantra works, you can maybe glimpse what the true identity of Protectors may be, as well. There's much else that can be said about the actual practices of protectors, if the student is empowered and engaged in the practice. Not appropriate to discuss here, though.
"Absolute Truth is not an object of analytical discourse or great discriminating wisdom,
It is realized through the blessing grace of the Guru and fortunate Karmic potential.
Like this, mistaken ideas of discriminating wisdom are clarified."
- (Kyabje Bokar Rinpoche, from his summary of "The Ocean of Definitive Meaning")