Is there any issues at all with having cans that are not full? Not sure if the sloshing around is any impact on the relative safety? Also what about the summer time? Are there additional concerns for the heat in some areas that the cans are exposed to?
It would seem that a good policy for safety and fresh fuel, may be to fill the cans prior to a trip and upon the return empty the remaining fuel back into the tank.
Also, is there an advantage or disadvantage to keeping the fuel, and the weight on the back of the rig while off road, versus moving that weight into the tank as soon as there is space?
Technically, the sloshing will make the fuel evaporate faster. This could lead to eventual reduced fuel quality (over a period much longer than you should leave the gas in there, though).
Indeed, I would definitely rotate the fuel through the tank once its purpose as an external source was fulfilled.
And yes, unless you need the fuel for extra equipment or perhaps to help other stranded vehicles, I would put it in the tank before aggressively offroading, once there is space. The factory fuel tank will distribute that weight much lower and more centered between the axles, and will likely be more protected than a jerry can on the back. Yes, a rotopax tightly secured to a high-end rear bumper is probably safer from puncture than a, for example, thin and unarmored factory fuel tank when traversing jagged rocks. But, if you puncture your gas tank, an extra 2-4 gallons of gas on the back of your vehicle isn't going to do a lick of good anyways, heh.