As all the previous advice indicates, F.I. is a plus, not a negative.
So Damien, you are an enduro rider, but do you have much experience with long distance bike travel into "3rd world" situations?
I think your Maroc warm up ride is a wise move. This will allow you to figure out solutions to the things that don't work out, that break, fall off or whatever.
IMHO, you're biggest probs with the 690 will be carrying luggage, fuel and water. I've ridden the 690 off road, great bike! But no real sub frame? 14 liters of fuel is more than the stock tank capacity, no?
14 ltrs. should allow about 140-150 miles? Not bad, but for Africa you might want a bit more? F.I. gives terrific fuel economy, a big plus over carbs. But if you go WFO all the time or if you're running a Race Map in the F.I. ECU, then economy can suffer. I'd go with a very conservative "lean" map for travel. Maybe KTM can help with this.
Packing light will be important, but honestly, in very rough going carrying luggage can cause probs. Things break, come loose, catch fire and are lost. Not many have done RTW type travel on the 690, at least I haven't heard much about it.
Speaking of going light, you don't want to end up like these German guys