can you try with "only look for js in head" and "only look for css in head"?
alternatively you can dive into the (non-autoptimized) javascript and look for something (a comma or a variable or ...) which causes autoptimize to see the aggregated javascript as different. an example would be a wordpress plugin which outputs a different variable for each page/ blogpost. this will indeed cause your cache to grow significantly. by excluding that javascript, you will be able to better control the cache size.