We made an evaluation of an isolated application where we wanted to grant an autonomy to cover the load, only through batteries, for a certain amount of time in any period of the year (with no production from reneweable and genset). To allow this, we did not find an easy solution and had to fix a minimum SOC of the battery which covered the load (that was constant) for that period of time. If there was a "battery reserve for autonomy" input it would have been easier. Maybe there was an easier way to work but we could not find it.
HOMER does calculate the battery autonomy, and displays it on the Battery tab of the Simulation Results window:
HOMER calculates the autonomy by dividing the usable nominal capacity of the battery bank (kWh) by the average primary load (kW).
If you wanted to enforce a minimum battery autonomy, you could determine how many batteries give you that autonomy (by doing the division yourself or experimenting in HOMER), and then simply prevent HOMER from considering fewer batteries than that.
Note that HOMER bases its definition of autonomy on the capacity of the battery bank, not on the amount of energy that it contains at any moment. If you want to ensure that the battery bank always contains a certain amount of energy (i.e. stays above a certain state of charge), the best thing to do is probably to specify the minimum state of charge, as you did.