Hi Andee,
CODAP supports multiple y-axis attributes for scatterplots because it is such a common use case. While I’m sure there a many situations like the one you put forward where it would be useful they just don’t come up among our audience. (You’re the first.)
Incidentally, I couldn’t resist creating this (unsatisfactory) workaround by superimposing two graphs, the top one with a transparent background.
Bill