Xcode 10 offers two build system modes: new as default, and legacy. However, the new build system doesn't index the libraries correctly when targeting an external build system, which is used by embedXcode.
So the build system needs to be set to legacy.
Once this parameter is set, the normal procedure Prepare the Project indexes all the libraries and provides the contextual help, as shown on the right.
I've modified the project preparation underlying utility to perform that setting automatically.
Let's hope the final release of Xcode 10 will fix that issue.
UPDATE No luck, final release doesn't fix this issue. So I opened an official bug with Apple, referenced 44452705.