You could certainly ask, but often times it's a logistics issue at big airports. When you return your car in the return lanes, there are probably dozens of cars in the way, you'd never be able to pull out again.
If you want to try this, you'd have to go to the customer parking area, do a manual return, and see what you can work out.
If this were a small location or a local edition, it wouldn't be a problem.
One thing to note, don't let them know you want to keep it because of the upgrade. Just ask if it's possible, you thought it'd be easier. If they think you want to keep the upgrade, they'll ask you to pay for it.