Dual battery mods are generally the ones that have resulted in venting, flaming, and explosion. Single battery mods are much safer. If you install two batteries in a mod and one is charged at a lower level than the other, the two will attempt to drain current from the higher charged battery to the lower charged battery, similar to two unevenly filled tanks of water connected by a hose. This happens are a high rate and Li-ion batteries don't like and can't withstand rapid charge rates. Heat is produced and failure usually occurs. Using a dual battery mod is playing with fire. One day you might install a charged battery with a dead battery by mistake. When you press the button, the two try to equalize and venting and hissing starts. I wouldn't do it. You are depending on the protection circuit to stop it once it starts. That might not happen.
It only works like you described in parallel setups, which are very rare outside of DIY Modder's builds.
In a series (aka "stacked") setup it is very common for one battery to drain faster than the other even if they start off at the exact same voltage. Effectively the exact opposite of what was described.