So far I've only seen a cell holder that was fitted for a cup holder. It it is made like a regular cup holder insert but is made of rubberized material, and it has slits in the middle where you can slide in a couple cells & some pens.
One idea might be to try one of those small dashboard anti-slip cellphone/coin mats and cut it to size to fit/secure into the handle slot. Alternately take one of those, cut it to size, and secure it on the bottom of the handle opening.
I hear ya about using that area for storage because I forgot about using the same space on my Escape's door. With the Ex, between the center console and the front console, I've had enough space to put my stuff and so far haven't made the mistake of dropping something through the door handle.