I accidentally discovered a perfectly fitting cover for my APM stack:
Yup - a cold-cuts box.
I am using a set of thumbscrews to hold my stack to the hexacopter frame , and the cold cuts plastic box fits over the thumbscrews perfectly. The cover doesn't budge in a hard landing or while carrying the hexacopter.
And it looks cool in the dark. (Not that I am planning night flying).