The intonation system is only relevant for a small amount of mediaeval music, e.g. stuff performed with a harp or organ where Pythagorean intonation was natural. It made more difference later on - Renaissance and early Baroque music really does need meantone, and it still helps with relatively recent folk songs.

The mediaeval modal system was not very relevant for secular music, and nobody at the time thought it was. It was designed to organize liturgies.