ok - the error messages are gone in the development version.
However, back to the initial problem: the fact that I got error messages means that polylang can read the wpml-config.xml, so it's in the correct folder. Removing the lines about taxonomies also removes the error messages and the wpml-config.xml works with the old version of the Pytheas theme. So I believe the problem with the strings not showing up in the string translation table must be linked to the new Pytheas theme...