Modules that are built automatically at setup, like Paths_PACKAGENAME or others created with a build-type custom, appear on 'other-modules' for the Library, Executable, Test-Suite or Benchmark stanzas or also on 'exposed-modules' for libraries but are not really on the package when distributed. This makes commands like sdist fail because the file is not found, so with this new field modules that appear there are treated the same way as Paths_PACKAGENAME was and there is no need to create complex build hooks.
Just add the module names on 'other-modules' and 'exposed-modules' as always and on the new 'autogen-modules' besides.