I'm learning that you have to change scales to cover the changes in this instance Dm Pent and A Harmonic Minor work well. Maybe I'm too literal minded but when I hear chord tones instead of scales...as if they aren't degrees of a scale! I'm not singling you out by the way, I see it phrased that way all the time.
Yeah, there's a bunch of different ways of thinking about the same assemblage of notes. You can think in chords, keys, scales, modes, tonal centers, arpeggios, etc. It's all a bunch of patterns, but if you just think in patterns, it can be kind of lifeless. The trick is to know the patterns so well you can forget them and just play.