Surpress "Declared and used flag sets differ" warning when `build-type: Custom` is set

As flags can still be used by the file's `Setup.hs` package, this warning can sometimes be spurious (the `Setup.hs` file may behave differently depending on whether the flag is set).

Start by locating the implementation and tests for the "Declared and used flag sets differ" warning, then inspect how build-type: Custom and Setup.hs packages are handled. Done means the warning is suppressed for this case without changing flag behavior; add or update coverage for a Custom build that uses flags in Setup.hs.

Written by the indexing model from the issue text.