Two 18650's are 7.4 volts correct? So you're saying two CR123's stacked are still 3 volts and not 6 volts?
Well the term 'stacked' is just a loose figure of speech. We're really talking about series vs parallel connected batteries. Let's say we're using CR123 batteries of 900mAh and 3.0v (nominal voltage) each:
Two connected in series will give us 6.0v and 900mAh capacity at that voltage or three in series will give us 9.0v and 900mAh capacity at that voltage. Conversely;
Two connected in parallel will give us 3.0v and 1800mAh capacity at that voltage and three in parallel will give us 3.0v and 2700mAh capacity at the stated voltage.
The M6 uses 6 batteries divided into two sets. Each set consists of 3 batteries connected in series (9.0v, 900mAh). Those two sets as a whole are connected in parallel or "3s2p" as what many here like to call it and that therefore gives us the total of 9.0v and 1800mAh capacity at that voltage.
From that point onwards, things get tricky as you may have read about how batteries 'sag' their voltage under load and then there's also voltage 'drop'. Voltage 'sag' at startup isn't that much of a concern for most LED lights nowadays. Rather, voltage 'drop' as the batteries deplete is more of a concern. Lithium primaries generally start at around 3.2v and will drop to below 2.8v by the time they're empty. Li-ions have a nominal voltage of 3.7v or 3.6v but fresh from the charger, they're usually around 4.2 to 4.1v each and will drop to below 3.6 or 3.5v when they're close to being empty.
Voltage 'sag' (for LED lights) starts to be important towards the end of a battery's life. A lithium primary that reads 2.8v when taken out of the light for measurement can be well below that once back into a flashlight and subjected to a load. So voltage 'sag' and voltage 'drop' will have to be taken into account to determine how to substitute lithium primaries for lithium-ions.
So if we do the math, an M6 starts out at around 9.6v when full and around 7 or something volts when empty. If you take into account voltage sag, then the batteries may be as low as 6 volts when nearing the end of their life. The heavier the load, the more the batteries will sag their voltage. Two li-ions in series will start at around 8.4v when full and will also drop to around 7 or something volts when empty and once again with voltage sag, may be as low as 6 volts or even lower if the load is heavy.