Here's what i think/read/personally observed...
matching batteries out of the chute is generally a good idea. the internal matched characteristics of the batts (max charge/charge rate/discharge rate/internal resistance, etc...) should match well. this is a no-brainer.
so, pairing a new battery A with a one year old battery B (which has many more charge cycles on it than A) --
even tho they both charge to 4.2 on your charger- might be a bad idea. why? the older battery's chemistry has changed - it's internal resistance is higher, and will likely discharge at a faster rate.
regarding rotating top and bottom batteries. like many, i have
observed that the top battery discharges further/faster than the bottom one. others have seen no difference. my theory is that this effect gets magnified if your batteries get over-discharged. (not a theory i want to spend the $$$ to test, tho

)
so, to me the bottom line is that not doing the pairing/rotating/happy crap will probably reduce the useful life of the batteries, but isn't the safety issue that some refer to...
although, i do believe reverse-charging is possible, i think the stacked-batt horror stories are pre-safe chemistry batteries utilized by fools in devices that were not designed for safe stacking.