By reading something about the acoustics of the romanesque, gothic and baroque churches in Meyer's "Acoustics and the Performance of Music" book, I might understand the difference between Maria Strassengel and Pernegg a bit better.
Due to the abundance of wooden structures, rised floating floors and galleries, baroque churches tend to be more reverberant in the middle frequencies, while the older churches had stronger bass frequencies reverberation. Pillars also create additional reflections.
This means that baroque churches, with their reduces bass and emphasized middle frequencies, are more transparent, due to the increased intellegibility of the open vowels (ah, oh) and the reduced masking of bass voices. Polyphonic music, predominant at the age of their building, is better perceived in baroque churches. The brighter color of walls also helps in receiving an idea of brightness and transparency.
Pernegg already relies on a baroque design, and was originally built during the golden age of polyphony. Its designers may have had a clear acoustic idea in mind.
So, I would say: solo instruments and voices, or music demanding for denser and darker reverberation, seem to be better placed in Maria Strassengel; polyphonic and transparent music should live better in Pernegg.
Paolo