As for Crete Armenoi, as I mentioned upthread we indeed don't know her provenance. To repeat, given how many "TSI like" samples pop up all over, she could have been from Italy, the Balkans etc.
Then there's the fact that it's a low quality sample to consider.
I think that to get a clearer picture of affinities, both the Northern Alpine, German Bavarian samples and the Balkan samples should be included in analyses. To use just one or the other may skew the analysis.