One additional thing to note is that most of the time the upper rune keepers give you the same as the lower ones. If you are not specifically trying to get higher runes then just click on the apprentice rune keeper at 8,000 a pop you will get far more total runes than the same cost doing auto rune. Fill the rune chest and sell all. That gets rid of the junk ones. you get 30-60% good runes that can be combined to form higher level ones.

Also note that if you are selective on what you combine they carry over a higher percent of the experience. Test it yourself. A single virgin mountain rune will transfer more to a mesa rune than other runes. If you are willing to put in the time you can get more power than if you auto everything.

It is just like auto grind versus picking the fights and watching them. You get more exp than just if you auto then walk away. because the guild techs and Epic Equip bonuses don't count when you are on auto.