Best practices for baking experiment 'design'?
It is no different from other prototyping processes or exploratory research. You are not confirming a scientific hypothesis here, you are actively searching. So the most important thing is: fail fast. 

So, for the question of mini batches vs. large batches, you certainly need mini batches. And in cooking it is more important than in other fields, as humans have a very poor ability to remember or record sensory qualities. In tasting two muffins side by side, you will notice differences which would not be obvious from notes from previous batches. 

Another thing which people find hard to remember: beat the Not Invented Here syndrome! There is a lot of information out there about which ingredient does what, which ratios are good for a given type of baked good, etc. It is boring to research them if you could be baking instead - but in the end, experimenting alone in your kitchen without theoretical background will never give you results as good as those created by teams of specialists who have been doing this their whole life, and using other information sources beyond primary experimentation. 

So, as with any good research, formulate your question first, and be specific. Then search for answers to this question. Only after you have found the theory, experiment how it applies to your recipe. Randomly changing things and hoping that you will hit gold is what many people do, but it is the opposite of a best practice.