My company has recently acquired the license for unity caching and I noticed that the uncompressed asset bundles are stored in cache. Is there anyway to store the compressed asset bundles instead?
No, this is currently not possible. Loading the AssetBundles uncompressed was chosen to make loading as smooth and fast as possible, as the decompression actually takes some significant CPU time.
When downloading AssetBundles from the web this is usually not such an issue, as the download will typically proceed slower then the decompressor, thus only compressing small chunks at the time. But when you want immediate access to the cached data, without slowing down the game while loading, storing data uncompressed is the most efficient solution, so it seemed like a reasonable tradeoff between disk space (cheap these days) and performance.