It is common nowadays for manufacturers, not just Toyota, to save both money and weight, by not sprayimg lacquer and topcoat on some areas which are usually not in view.
This practice was started by Mazda when they introduced the 2007 Mazda 2 and which was the subject to intensive weight saving compared to previous models.
For example it is common for engine bays, spare wheels wells, etc not to be given topcoats.
I would probably suggest that the wheelarches, if they don't have topcoat/lacquer applied, will still have stone guard paint applied, so will still be well protected.
As I said earlier, pictures may help.