I bought my RV with hopes to be able to take my pets with me when I follow seasonal work, and I just finished transforming the bunk area into a pet corner.
I had custom cages built by Martin's Cages to perfectly fit the top bunk with room to maneuver. They were priced comparable to the cages in their catalog. I left the mattress on the middle bunk, since it's the only one with a window. My cat loves to sit there in the sun. I put waterproof contact paper on the bottom area and rugs there for the cat food and litter box. Everything fits exactly how I pictured it would.
My family is big enough to make use of bunks, but most of the members are four-footed.