I thought the original problem was un-crushed bottles, in which case the bottles have a fixed need of a surface area in the box. When bottles are explicitly placed into a box, the dimensions of the box will affect the robotics for placing the bottles in the box.

If the bottles are physically broken, as in missing parts, and then always crushed, then surface area doesn't matter anymore. It will all come down to weight or volume. Ten/fifteen bottles sounds like a very small amount if storing crushed glass. If would be more logical to have a way larger container and not care at all about the bottle count. Let the container shake to get an even distribution of the glass fragments, and then only care about the weight in the container. When reaching 25kg or 100 pounds or whatever, replace the container with a new one.

With crushed glass, there isn't a need for any optimization steps. It is best to just go for the KISS (Keep It Simple Stupid) design methodology. Using a scale for the weight of the container, the system can handle a power loss without having to be able to remember how many bottles that have been placed in the box. It is enough if the robot arm that picks up broken bottles from the conveyor belt has a sensor so that it knows if it is currently holding a bottle to be crushed, together with the weight sensor. And there wouldn't even be a need for a robot arm. It would be enough with a ram that just pushes one bottle (or bottle pieces) of the conveyor belt.