I believe all the fear mongering about stacked batteries came from a combination of factors:
Using unprotected Li-Ion batteries: These explode quite violently if something goes wrong, protected Li-Ions will shut down if too much current is being drawn or the voltage drops too low. Protection circuits on batteries can fail though, so Li-Ions are still more dangerous than IMRs. The IMR batteries used in these VV/VW devices are even safer than Li-Ion, they will get hot and vent, but not explode like Li-Ions. Not only that, but they are capable of a much higher discharge rate, which means they can put out tons more power without exceeding their safe discharge rate.
Using mods with zero protection or regulation: Several issues come up because of this. First of all, there is no short protection, so if your device shorts out you can nearly instantly fry your battery, which if using unprotected Li-Ions can cause a small explosion. No real amp limit built into the device, so if you use heads with a resistance too low, again you can fry the battery. Also you don't have any sort of low voltage cut-off, so it's possible to drain the batteries past their safe discharge voltage.
Using spacers either between the two batteries, or on top of the positive post: Most all devices use the body of the PV as the negative connection to the heads. Using a spacer on the negative end of the battery is perfectly safe and can't cause any issues. But if you use a spacer between stacked batteries, or on top of the battery stack (positive terminal) this can short your batteries if it happens to wiggle around and touch the inside of the battery tube. Sometimes people use thin magnetic spacers between the two stacked batteries because they are flat-tops and won't make contact otherwise. I personally would advise against this, as the risk of shorting is always there.
When stacking IMRs with a protected and regulated device there really isn't any more risk than when using a single battery. Using any battery, whether it be a AAA or a 26650 beast it will have a risk associated with it. But when stacking IMRs in a protected and regulated device the risk is really quite minimal.
It's good practice to not use two different batteries of vastly different age, or of different charge status (using a 4.2 and a 3.6 battery at the same time, for instance) But it's not really necessary to keep your stacking batteries as a joined-at-the-hip pair. The issue with using batteries of different charge status is that you could over-discharge one of the batteries.
If the device's low battery safety cuts off the dual battery voltage at 6.4v which would be 3.2v per battery (the voltage you can safety take each battery down to) But if you are using one fully charged battery (4.2v) and one less charged battery, the cutoff won't kick in until the lesser-charged battery is well below the safe cutoff voltage. So that's why you need to make sure both batteries are charged to the same level when stacking.
Using vastly different aged batteries is also a bad idea for basically the same reason. A much older battery won't hold it's charge as long, which means its voltage will drop faster than a newer battery. If this happens you can run into the same issue I just described, one battery being over-discharged and potentially damaged.
But that doesn't mean you can't use them by themselves sometimes, and then stacked other times. I mean, if you want to only use a single pair of batteries for stacking, and never use them separately, more power to you. But there isn't any risk in using them separately and then stacking at a later time, assuming they are of the same general age/use and both charged to the same level.
