Been wrestling with this exact scenario on my setup, so thought I'd share what I've learned.
Running a smaller generator (mine's a 5kW Yamaha) with the MultiPlus II charger can be inefficient if you're not careful. The issue is that the Multi wants to ramp up charging aggressively, which means your genset has to work harder and burns through fuel quickly. In spring and autumn, when I'm not getting consistent solar, I've had to develop a workaround.
What I've found works is running the generator separately to top up via a basic MPPT-style charge controller set to a conservative amperage limit — around 30-40A depending on battery state. The MultiPlus stays in inverter mode or UPS mode during this time. Once the batteries hit around 80% SOC, I'll switch over and let the Multi finish the job if needed, though honestly the genset usually switches off by then.
The alternative approach some folks use is disabling the Multi's charger function entirely when running the generator, and instead using a dedicated charger (like a Meanwell or similar) set to a fixed output. Less elegant but genuinely more fuel-efficient on small gensets.
Has anyone else found a cleaner solution to this? I'm curious whether setting the Multi's charge current to a lower limit actually helps, or if it's just delaying the inevitable inefficiency. Also keen to hear if anyone's tried running their genset into the AC input with the Multi in passthrough mode — theoretically it should work but I've never risked it.