TL DR: This isn't how it's supposed to be. They should be the same from side to side ... however ...
However, stuff happens. As Solar Mike aluded to, things happen on the assembly line which can give you the wrong options. More than likely the dealership never even noticed, or maybe they did notice and that's why they made it the convenience vehicle.
Before you go down to the dealership and demand getting them changed, in the US auto sales market (in most states), there's a thing which you probably signed called a "We Owe Slip". This is a piece of paper you sign at the time of sale of used cars which states if the dealership owes you anything on the vehicle. This gives you a chance during the purchase to state, "The salesman promised me a set of floor mats for my truck!" and gives you recourse if they don't provide them. It is a legal document between you and the dealership which protects both of you. If you didn't sign one stating you were owed getting the correct door handles, you're basically out of luck in the demands department. If you signed one with nothing on it, you are agreeing with the dealership you are not owed anything. This, in essence, prevents you from going back to the dealership stating you were promised stuff which wasn't delivered.
With that said, the best you could hope for if you are really bummed about this is to go back and ask nicely about getting them changed out. If they say, So Sorry Charlie, you're basically out of luck, unless you want to pay for them.
On the other hand ... if this was sold as a "new vehicle", you may actually have recourse. What is considered a "new vehicle"? One which has never been titled before. Many dealerships will put dealer tags on vehicles such as what you're describing and drive the wheels off of them (IOW: mileage doesn't count). They don't have to pay for licensing or taxes or any of the other BS while they use the vehicle. So if it was a new vehicle sale, manufacturers have what's called an "adjustment period". During the adjustment period, you can come back to the dealership and get things ... well ... adjusted. This may apply in your case. The normal adjustment period is 12 months and gives the consumer a way to get little things fixed on the vehicle. If there's a scratch in the paint from the sales lot, or if exhaust is rattling for some reason, you can get it fixed, no questions asked. The dealership doesn't pay for this, the manufacturer does.
Along with this, if it was sold to you as new at the point of sale, the manufacturer's warranty starts at that point as well. If there was 6k miles on the car, your warranty should be covered out to however far Ford covers, plus the base mileage of the car when you bought it. This ensures the consumer gets the warranty which they paid for and can discount the miles on the vehicle which were there when they purchased it ... it works for 6000 miles as well as it does for 60.