Ah, that explains a lot-- it's a sandboxing thing:
https://developer.apple.com/library/mac/documentation/security/Conceptual/AppSandboxDesignGuide/AppSandboxInDepth/AppSandboxInDepth.html
When 1Password is a MAS application, it has to be sandboxed, thus the obscured "Containers" directory that holds the bookmarks-default.json. I'm guessing the LaunchBar indexing rule for for the 1Password file isn't looking in Containers directory, just in the original directory.
https://developer.apple.com/library/mac/documentation/security/Conceptual/AppSandboxDesignGuide/AppSandboxInDepth/AppSandboxInDepth.html
When 1Password is a MAS application, it has to be sandboxed, thus the obscured "Containers" directory that holds the bookmarks-default.json. I'm guessing the LaunchBar indexing rule for for the 1Password file isn't looking in Containers directory, just in the original directory.