You know, that's a really good question.
Your 5.0v box mods are usually resisted to 5.0v and the batteries installed in series. When batteries are in series, that means you are doubling the voltage but not doubling the mah. When batteries are installed in parallel, you keep the same voltage of a single battery but double the mah by having two of them. Stacked batteries in a tube with a mechanical switch are in series.
The best part of your question comes down to "Is there a difference between stacking batteries so they actually touch each other versus having a pair of batteries in series but not physically touching each other?" Does the fact the batteries touch each other make them in some way more dangerous than an electrically identical circuit that has the batteries side by side rather than one above the other?
Well, there is no difference. Weather or not the batteries physically touch each other to make series has nothing to do with their behavior. One will drain faster than the other no matter what, and one battery being over-drained is what seems to be being blamed for the incidents that have occurred. (and that baffles me a little too because these events supposedly occurred with batteries fresh off the charger, so are they saying that series batteries have undergone too much strain from overdischarge or are they saying that somehow one battery drained instantly? I don't understand their logic at all)
Some people say the battery closest in the circuit to the atty (the top battery if it were a tube with batts physically touching each other) will drain faster and some say it is the battery that has the least internal resistance. Anecdotal evidence exists to support the top battery idea. Lots of people have noted their top battery draining faster no matter which battery they have had one top (and they keep track by labeling their batts). An electronics class I took in the 80s leaves me with the thought that it should be the battery with the least internal resistance... so my only explanation is that that there is no internal resistance difference in most pairs.
As to safety: Well, according to ECF, the only way to make batteries dangerous enough to cause any severe physical harm is to put them in a tube without enough venting. They seem to think that since a box isn't sealed like a tube, there is ample venting opportunity in the event of a battery failure. That probably is correct to at least a certain degree.
The one thing that might make batteries being on top of each other more dangerous than being side by side is perhaps some box designs might be helpful to keep a "vent with flame" episode from affecting the second battery to the same degree as if they were stacked in a tube... but then, batteries don't just vent out the top or bottom. They can just as easily and might even be more likely to vent out the side. I guess then it just depends on which side is facing the other battery.
Anyway, series is series weather stacked or side by side. I do happen to be someone who isn't afraid of batteries in series and I think the injury accidents that have happened are due to low-quality counterfeit batteries and there is very little risk involved with series batteries that aren't cast-offs, counterfeits, or just plain junk to begin with.