From your question, it doesn't seem that the proximity of the train to the property you are considering is a deal killer. If you're open to the concept, I would suggest insisting on a visit when trains are approaching (you should ask your agent to coordinate this). You can get the Metra schedule and coordinate a showing during that time. Pay specific attention to the train stop scheduling. A train may be louder if it's not stopping at the station near you (it may bypass that station and be moving much faster). Also determine if the line is shared by freight. You'll have to wait for one to pass, but freights can be significantly heavier than Merta rail and may cause more noise and vibration.
If these noises and sounds will not interfere with your enjoyment of the property, make an offer. You may get a great deal on a property that has adverse landmarks like rail nearby in a market with so much inventory.
If you find the opportunity, find out how the neighboring property owners feel about the concern you see. They are likely to be more candid because they are not currently selling (or more sound sleepers).
As for why they build in sub optimum locations and the lack of sound consideration in the design and construction, they must have built them in a very hot market when buyers are less sensitive. In cooler markets, buyers are much more particular about the details.
Best of Luck and always willing to be of service.