I am wondering if anyone sells a bonding pouch that is fleece on the inside and something more water proof on the outside? Maybe a material that jackets are made out of. Or does anyone sell one with some kind of middle layer?

What exactly are you looking for? Or maybe I should ask what circumstance would it require for them to need water proofing?

Any material used for a bonding pouch needs to be breathable.

There are certain water resistant materials that allow air to pass. In that case, yes it's possible. However, depending on the material, it may not be able to use it as a sleeping pouch in a cage. (Basically unsupervised )

Is this meant to be used as a bonding pouch or for traveling?

I can only seem to find fleece bonding pouches. I guess I am thinking more along the lines of flannel, or a material similar that might still be breathable, but urine won't go straight through. Not sure if this exists. Just figuring it might be nice if I'm out and about with a suggie.

When I make ferret bedding I typically do the bottom fleece, the middle layer with stuffing, and the top layer with cotton.

You can use flannel or cotton for the outside.

Normally they won't potty in a bonding pouch. If they become fidgety, you may have an accident.

Be sure to use a good quality flannel or cotton. Also be sure to finish the edge or pink the edge of the cotton/ flannel to keep it from fraying.