Well, 4 Eneloops powering an XM-L directly means that the LED is getting 4.8V, but, the battery voltage would sag under load down to a safe level, as you are seeing. I've seen an XM-L turn blue (white LEDs turning blue means that you're seconds away from frying it) from 3 NiMH cells, but ran fine on 3 alkaline batteries due to the fact that alkalines have a high internal resistance and that limits the current. Is 3.3A safe on an XM-L? Probably. As long as you don't see blue light you're fine, but, keep in mind that you are over driving the LED and that you probably will not get the rated lifetime out of it as a result. Then again, the rated lifetime of that LED is far longer than most of us will use up in our lifetimes so have fun with it.
Vf (forward Voltage) is the voltage of the emitter at a given current. As you increase the current the forward voltage rises. In a direct-drive setup, the voltage sag of the batteries under current and the Vf rise with current reach an equilibrium and you end up with what you end up with. With your DD setup, measure the voltage at the LED when it is running at 3.3A and you get the Vf of the emitter at 3.3A. Remove one cell and try it again and you'll get a Vf of that emitter at whatever resulting current you get from it.