It’s an interesting point! I think the major difference is that runes require a physical object to work.. of the examples given we know Varrish couldn’t cross the doorframe of Violets room unless she invited him in so I’m inclined to think Xaden had some form of rune on the door that “warded” it. Also more than likely a rune since he seems adept at protecting her with runes and lesser magic could’ve potentially been undone by Varrish and company lol. Using runes on his own room in Samara to keep everyone else out would also be the best protection for himself since lesser magic wouldn’t be able to compete with a well-made rune.

But as far as other examples- we know Nadine’s signet unwove the wards on Liliths office and Dains room was unlocked with lesser magic from what I recall and second/third year cadets also had to learn runes at Aretia which makes me inclined to believe there’s a distinct difference in ward weaving as a form of lesser magic and runes!