When I model a PV system that includes different quantities of batteries HOMER gives me the optimum quantity, but it doesn't make any reference about the specific configuration.
You are right, HOMER doesn't say anything about how many batteries are in series or parallel. That's because it doesn't know. As far as HOMER is concerned, your battery bank of 20 batteries has a kWh capacity that is 20 times bigger than an individual battery, and that's all it needs to know. It doesn't calculate voltage so it doesn't need to know anything about how the batteries are arranged in series and parallel.
If I were designing a system, I would choose the DC bus voltage that I wanted, and that would determine the "size of the strings", which is the number of batteries in parallel. For example, if I was planning to use a 48V DC bus voltage and I was modeling 2V batteries, I would need 24 batteries per string. So in the Sizes to Consider table, I might put 0, 24, 48, 72, 96, 120, and 144. That would correspond to 0, 1, 2, 3, 4, 5, and 6 strings. If HOMER recommended only 24 batteries, then I might reconsider the bus voltage, and maybe try 12V DC instead. That means 6 batteries per string, so for sizes to consider I would enter 0, 6, 12, 18, 24, and 30.