I found them with #7952 but only tested native and samr21-xpro.

I don't understand the second commit. Are you renaming the package modules to pkg-X?

I am renaming the package root module to pkg-X yes.

For libfixmath for example: both the package root and the libfixmath directory Makefile have MODULE=libfixmath. For the package root its because the directory is named libfixmath.
So they both define the libfixmath module and both produce the libfixmath.a archive.

Currently everything is working because ar just adds new files to the archive and does not care that two modules modify it.

What I did, is rename the root directory module to some dummy name. It will produce an empty unused archive but not touch the real libfixmath.a one.

I am renaming the package root module to pkg-X yes.

Where do they get selected for linking?

They don't get selected for linking but they are empty libraries.

No source files in the module Makefile directory:

RIOT/tests/libfixmath$ ls bin/pkg/native/libfixmath/
0001-Move-to-RIOT-Makefiles.patch                                benchmarks  images      unittests
0002-Fix-warnings.patch                                          contrib     libfixmath
0003-Adapt-unittests-for-RIOT.patch                              fixsingen   Makefile
0004-Change-conflicting-module-name-for-pkg-root-director.patch  fixtest     README.md

And the produced library is indeed empty

RIOT/tests/libfixmath$ ar t bin/native/pkg-libfixmath.a
RIOT/tests/libfixmath$ 

They don't get selected for linking but they are empty libraries.

I see. Seems to me the package Makefile is more complicated than needed. That package's Makefile.include could just add the necessary folders to "DIRS", saving the empty module.

Anyhow, thanks for the explanation!

I also think that, in general, setting DIRS should be handled by the main and sub Makefile.include and not submodules Makefile but that is a separate task.