Why do stacked batteries create a problem? I use them in my Vamo v3 with zero issues so far. I stack the 18350's.
When you hit the fire button, current flows in the circuit and both batteries deliver fairly equal voltage and current in a series circuit. If one is dead but not at cutoff, when you hit the fire button the discharged one will begin to equalize current flow with the fully charged battery, but in reverse, in effect charging the empty battery very quickly. Heat results and the electrolyte can reach high temps in a hurry. Hot electrolyte in an enclosed case builds pressure rapidly.
IMR and Li-ion batts don't like fast charge or discharge. Both create internal heat. IMR can take such abuse much better than Li-ion. Some IMR batteries can take 10 amp draws for short periods without harm and can reach temps close to 500 degrees internally without self destructing. Li-ion tends to spew and vent when that happens. Go for the IMR batts when you buy.
Stacked batteries are fine as long as you don't screw up and install one dead one and one fully charged battery by mistake. As long as both are fully charged, you should be fine.
You are also fairly safe if your mod utilizes a sacrificial spring on the end cap. When the high amp load starts, it will heat up and sag, breaking the circuit and taking the pressure off the batteries, which will hopefully stop the heat buildup before the batteries turn into bottle rockets inside a metal tube.
for safety's sake, IMO you are better off using one 18650 as opposed to stacked 18350 batts. There's less to worry about. That's just me. The fewer batts I have to charge and keep up with, the better.
But don't take my word for it, read up here. This should be required reading for anyone using hi tech batteries.
Basic to Advanced Battery Information from Battery University