I noticed this when I would jam with other guitarists; they would always come up with stuff in Major or Minor keys. I'd ask them what scales they knew, and they would only know those two (except pentatonic which is still based on major/minor scales). It doesn't say their not good guitarists, but their music output was very limited. Next, I would play something and if it wasn't in those keys, they had a hard time putting something to it cause they were searching for the notes. Or they would come up with something very blandish, cause they only used major and minor scales. The inner ear works on how much it knows, if you have never heard a Locrian mode or practiced it. You probably won't think up something in that mode, cause you don't know it. Everything else is very hazy and clouded, although the idea is there is not concrete. You will always dominantly hear ideas in the keys/scales/modes that you know. The more you know, the more you can do! Knowledge is power, and the ear is based on your knowledge!
I believe understanding should come first especially when learning scales. Understanding gives you a nice foundation to use what you have newly acquired. Without it, it's just another pattern of notes, and how is that going to help you? I also believe you should start with the root when learning a scale. For learning and understanding the scale, the root gives you a solid foundation to build knowledge on. That why it's called the root. Later when you incorporate them into your music, you probably will never start with the root. If you’re learning a mode like the Locrian, watch starting on the 7th. You’re only playing the minor scale again!
Now as you said, a D7b9 can be approached modally. An understanding of which modal scales work nicely with the chord will give you a nice solid base to stand with. This is where theory is a benefit, especially when coupled will good ear training. The chord D7b9 contains the notes D, F#, A, C, and Eb. Two different scales work nicely over that chord. When I mean nicely, I mean they contain the tones that sound pleasant to the ear relative to that chord. One scale is the Spanish Phrygian scale, and the other is the Lydian Dominant Scale. The first scale contains the notes D, Eb, F#, G, A, Bb, C, and the second contains D, E, F#, G#, A, B, C. Together the notes are D, Eb, E, F#, G, G#, A, Bb, B, C. The only notes left out are the F and C# which would change the initial spelling to a Dmaj7b5. Unless this is what you first intended to have there, these notes are excluded and rarely brought back to give a discordant sound. The reason is the F falls in between the notes E, and F#. So you would have E, F, F#, and G boxed in the chordal sound, which is very discordant. Same with the C# that falls in between C and D. So you get C, C#, D, and Eb boxed together, not very pleasant sounding. If this is what you were looking for, this understanding helps that much. Next is which one to choose to play. There is no choosing!! Now if you know how each scale sounds, and you've learned them. Your inner ear will involuntarily choose the one it wants, cause it knows how each tone will interact with the sound. The melody you want to play will fall into one of these scales (modes), maybe both at separate points. The benefit is you will know where to start because your understanding is solid. Knowing all the scales possible gives you every angle to approach music. The base of music theory is understanding.
Modal composition is extremely rare as Griphon said. You may find it though, mostly in guitar solos. Especially metal, since metal solos are based on the art of Fugue. Want to learn how modes sound and how to use them, listen to and analyze Bach's music.
"My whole life is a dark room...ONE BIG DARK ROOM" - a.f.i.