That is one idea, true. But I would be concerned the charms would "fall" and become folded.
I store mine in totes that are wide enough to have 4 stacks of charms. Then I store them in stacks by color. Or if they are still wrapped together (package), I store those on their own stack. I'm not sure if that is making sense, but the clear tote at least allows me to narrow down which one I'm picking, knowing that tote #1 has blue, pink, purple, and green for example.
I'll be watching this, as I think many of us have issues with how to do this well.