Actually, I have no problem with two 600-800mAh 18350s lasting all day on a PWM mod.
The thing about a stacked configuration is that it's not so much about the fact that it can give you more power -- beyond a certain point no sane person would vape at those levels -- but about efficiency and accuracy.
In single 18650 mode the boost circuit has to engage. This draws power from the battery -- not a lot, but it does. It also has to put more effort into maintaining voltage under load, especially as the battery drains.
Stacked batteries do not need the boost circuit except when they collectively drain below 6V and 6V is needed, then both the boost circuit and voltage regulator have to engage. (But if you're using your batteries down to 3V each you're cutting it pretty close to critical and the cutoff should kick in around there anyway.) Instead it just has to limit the current. This requires only the voltage regulator, so right away it uses less power. Furthermore the regulator has an easier time of maintaining voltage levels under load because it doesn't rely on the boost circuit to nudge the voltage higher, it just has to limit the current. So the vape experience is much more level across the charge and overall superior to the vape experience under the boost circuit on a single battery.
Yes, there are increased risks to using a stacked configuration, but as Ictinike pointed out, as long as you pair your batteries and keep them well charged, the risk is extremely minimal.