Not having the ability to set the start and stop states of charge for generators independently of the battery minimum SoC. Reason is to enable a battery system to coast through the night if a quiet perod is required (no generator run) without the system shutting down.

You mentioned that in some cases the generator cannot run overnight so the system needs to be able to operate through the night on battery power.  Please note that HOMER will let you schedule the operation of the generator, so you can force the generator not to run overnight.  What you cannot do is force HOMER to charge the battery to a certain state of charge in the evening, so that when the generator does go into forced-off mode, the battery bank is fully charged.