I'm doubtful that the runes actually do anything, it sounds like that one door opening is a loading error rather than something intentional, but I did notice that the Y shape reminded me of a plasma pistol. Turns out the angle of the Y fits just right in the reticle of the plasma pistol. Dunno if anyone else noticed that yet, but if there is some secret maybe it involves plasma pistol. I tried messing around shooting glyphs in different ways but didn't get any kind of response.