The cape does not dissapear, nor does the elytra use the cape texture when using a cape. I know it's at the very least possible to do, since the Winged mod does do this.

NOTE: the winged mod doesn't use the elytra texture as far as I know, and personally, I don't care about the elytra texture being rendered, but that's your decision, especially since you're the developer, and I'm just some dude trying to play modded minecraft...

fixed in the next release