Just think of the VF Tuner Tune as your new baseline ECU map.
Best example I can think of is a Valet setting on some cars. When set to valet mode, the tune does not change, but additional settings/restrictions are placed over the baseline tune to retard throttle response. The tune has not changed, but there is an OEM setting that changes how throttle response and shifting will respond.
as for the difference, if VF Tuner does provide the aforementioned maps (Towing, MPG, etc) and on the go map-switching, the OEM modes might be redundant and even limit the already specialized map. For example you are on the mpg map, but choose the sport mode on the GX dial. I would think that once you commit to make the switch to Custom maps through VF Tuner, you would no longer need to use the OEM settings and rely on VFTuners map settings to achieve what you want.