Best space-efficient freezer system?

I don't have a dog so I don't know how big a serving of food would be, but could you use muffin tins? I'm thinking a silicone one would be ideal--batch out the food into the cups, freeze until firm, then unmold and place the portions into a plastic bag. Then thaw out however many portions you need.

Re: washing out plastic bags--I do this all the time. I use hot soapy dishwater in a basin and wipe out the inside and outside of the bag. Rinse in hot water in another basin and prop over an empty bottle to dry. They dry overnight.

I do not agree with premise that you would not need to wash the bags. Any recipe I have seen for homemade dog food is not going to be sanitarily contained by butcher paper. And presumably the outer freezer bag could be sitting out of freezer for up to several weeks. I can't really think of an alternative to plastic ( or some type of rigid containers) or freezer bags. The only suggestion I can offer is if you currently freeze the food in one day allotments you probably could freeze 2-3 days worth in one package. Not as convenient as you would have to then give it refrigerator space and scrap off the exterior as it thaws to serve. How long it would hold in fridge might depend on whether you are using a cooked or raw formula. I think it is very common for people making dog food to acquire an inexpensive 2nd freezer exclusively for dog food. I have made a lot of dog food in the past but always made it every few days and fed fresh. Ultimately I abandoned making dog food and switched to a mostly prey model diet which is much less time consuming.

You could wrap daily portions in freezer safe butcher paper & put those in gallon freezer bags. You can toss the butcher paper & reuse the bags without the need for washing. Just label well.