Is it possible for any impurities to get through the apple peel?
The answer I got from Jan Kolář of Charles University:

The spores of fungi or bacteria in apples don't just emerge from nothing, they have to get into it from the surroundings. I often see apples, which rot while still hanging on the tree, the hole needed for the infection of the apple is usually made by a worm. The problem of the apples near roads isn't that they would rot. Indeed, plants can absorb all kinds of harmful substances from soil, water or air, including heavy metals, chlorinated organic compounds or organic compounds from the exhaust gases of cars. How much and which substances, that usually depends on the type of plant (specifically on where it stores most of the substances).

It's not enough to wash an apple because the impurities are absorbed in the fruit itself as well. And on the surface of the peel, there are waxes and other unsolutabe substances which can absorb toxic aromatic carbohydrates from the exhaust gases, and can't be simply washed off.

The greatest risc near the roads used to be contamination with lead because petrol used to contain it. Many of the plants can recieve the lead and hoard it up in some organs. Now, when the lead petrols are forbidden, the biggest risc pose the fumes from the diesel engines. So I'd rather not eat fruit near the roads (especially near the busy ones).