This is because the improvements have this tag on them <HideInHiergamenon>1</HideInHiergamenon> and that is because they do not want duplicate entries for the Air Altars and such. Basically you would see two identical copies in the Hiergamenon, with two different bits of information.
I've suggested they rename the altar, shrines, and temples for those with binding trait, by calling them Air Grave Altar or some sort of other name. They could think up of something that they like. Then you would have two copies in the Hiergamenon with distinct names, it would show up on the research tree with those names, and the information displayed for the "same" type of object represents the appropriate information with the binding skill.
I think this is a win win win situation for renaming these Shrines and Temples.
