Here is my solution to batter covers + Mud. It works.

[BOTG]

The velcro covers the mud port at top of battery, and stops it coming off, it also doubles up as a spare inner tube holder.

 

[Swissete]

Lol, good idea

 

[Slymobi]

I've adopted ( before I seen your post honestly ) a similar idea with velcro but also holding a downtube mudguard which does a good job. Pic is an older one but I've recently added an extra wrap of velcro to cover the top lock on the cover too.