This is due to how the dungeon system (dev naming convention) was created for what you know as 'Elite Dungeons'.
Both the 'Zamorakian Undercity' and 'Sanctum of Rebirth' make use of this system, but with additional features such as enrage, unique reward chests, different group sizes, etc.
The dungeon system will continue to be used going forward for content of this type, and while working on the Sanctum we definitely discussed decoupling the save state data so that you can progress the dungeons independently however it was out of scope for the project in the end.
We have a task in the backlog to look at doing this at some point in the future.
TL;DR - Yes, we agree that they shouldn't share saved progress, and would like to resolve it at some point.