I might be off base here, but I think the difference between diatonic harmony and non-diatonic harmony (chromatic for lack of a better term) is part of the confusion. There is a large portion of musicians who do not create diatonic music. They combine chords based on how they sound together rather than combining chords that are ACTUALLY part of the same scale (pop and rock are two examples of this). I blame this on guitarists learning generic chord patterns rather than theory. Now a bass player struggles to link the theory that expert musicians tell them is important (ie: scales and modes) but cannot apply scales or modes in the CONTEXT that their music is being played. I believe this is why many musicians try to incorrectly apply modes to chords (I am very guilty of this). They try to affix meaning to the all important mode but the music is not based on diatonic anything. The problem is further compounded by countless instructional materials showing diatonic relations of modes or chordal relation of modes, neither of which are necessarily right for this type of music. Perhaps a person wanting to understand modes should be pointed in the direction of chord building based on the modes. A I in C ionian is going to be different than a I in dorian. A II in ionian is going to be different than a II in phrygian. My theory learning experiences were centered around writing out progressions on paper: start with the key signature, make your progression based degree (I, ii, iii, IV, V, etc), write out the chords degrees based on available notes, make your melody fit with the chord progression. I think it's this link to the diatonic portion that is confusing the modes for newbies.