Efficiency due to long run times on heating equipment is because of less start-up sequences mainly. With mod-con boilers this isn't as much an issue as it is with say warm air furnaces. The circulator starts immediately and even the very first bit of energy that the burner produces is being transferred to the liquid (almost).
I did read your other posts about this system. I'm not quite sure I understand what you're meaning by the boiler is controlled by the outdoor thermostat. If you mean the boiler output temp is controlled by the outdoor temp, then ok, this is the outdoor reset function. As far as the boiler cycling on and off when the thermostat is still calling for heat.... it could mean that the input of the boiler can not modulate down far enough to match the heat loss of the zone(s) being heated. In this case the boiler will cycle on and off until the zone thermostat is satisfied.
As far as if this is a good way of operating the system.... It's the way it's operating and if everything is set up right it may just come down to the minimum firing rate of the boiler is still too much input for what your smallest load can use.