Well technically they are also not intended to be there, I haven't lost companions that I hired via the "intended" way, meeting them in a tavern, back story, pay. Only those that I added thru the console commands. Which is understandable because the game might think they aren't even truly there. But then again if it's a "feature" then that would make the companion command obsolete.
Edit #1: Forgot to add that it's an ironman playthrough with Birth and Death disabled, and also companion chance of dying in battle reduced by 100%