Ok, then the return is not at the Santa Maria Novella train station, it is near it but you don't have to go to the station.
The most important thing to remember is this: the drop off rental place is NOT in the ZTL but the street runs right along the ZTL, so you have to make sure you do not make a wrong turn when returning the car. Which means they don't have to communicate license plates to the city because you didn't have to go into the ZTL to get to them.
If you accidently do make a wrong turn and go into the ZTL, then you will get a fine. I've mapped the best route to get to them, the best thing would be to input the address from where you are when you're going to return the car and see if this end part coincides because it is the only way to get on to Borgo Ognissanti without going into the ZTL: you need to go into Via Il Prato, then on to Via Curtatone, take the Lungarno Vespucci and then turn left on to Via di Melagnano and left onto Borgo Ognissanti. It's just a bunch of turns because some of these are one way streets so you need to do this circle around the block to go down Borgo Ognissanti in the right direction.
Are you coming soon? In July further head on Lungarno Vespucci there will be construction works on the road so it will be closed, but it should be after the stoplight (at the bridge) where you are to turn left in any case, so it should not impact your route.
I lot of people return the car at the airport to avoid the return in this area, but since you're driving from Milan, by the time you get here you will have gotten used to the roads and streets so should be fine. You're preparing ahead and that will help a lot! Have a great vacation!