Part of the reason is because the theory grew up to explain the practice. What does that mean?? It means that the monks had sung their chants in a certain fashion for many centuries. At some point, the music theorists decided to try to organize what they heard and give the different scales used in the chants particular names. All of this ended up running together and getting mixed up with the Greek scales (which really were different and don't match the church modes at all!). See the end of the tidbits page for sites that have more info on the Greek theories - they are quite interesting!
It actually wasn't until fairly recently that historians figured out that the Greek scales & the Medieval Church Modes weren't the same! But when you think about it, it isn't surprising - there was no way to write down music back then, and no way to record performances, so all we have to go on are some instruments that survived and the writings of the scientists and philosophers. We don't really know what Greek and early Roman music sounded like!
And then to confuse things a bit more, our modern composers came along and wanted to work with the modes, but of course they didn't have the octave restriction that the monks had. So they figured why bother with the plagal modes; all they needed were the authentic ones: dorian, phrygian, lydian, mixolydian, aeolian, locrian, ionian - forget the hypo-this & that!
Thus we find that there are many different ways to refer to things, they cross over and they don't stay neatly in their categories.
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