This is true—having to manage multiple systems is definitely a con of using an external reference manager. Does something like using cite keys mitigate this problem?
Book Search is a great plugin. I used it for awhile. Combined with the popular movie lookup script, it can turn Obsidian into a useful reference manager.
A disadvantage I see to using Obsidian as a reference manager is that the metadata can get messy if you’re not careful. My tendency is to collect metadata that turns out to be unnecessary.
This is great! Thanks for sharing! I hadn’t heard of Bookends, but it seems useful.