1. The noise tolerance of a buyer will depend a lot on their point of reference. I know people that come from NYC and they think it is so quite in PJ. The occasional train passing by is of little concern to most people coming from the city. Many people are more concerned about the quality of the school system and shortening their commute in exchange for having a train passing by. You can definitely hear the train, so you need to check it out for yourself and see how you feel.
2. Resale values are very location dependent, and The Estates are in a prime location, with great schools and great commute. Your not going to change the location, so figure that is a constant in the value of the property and there is nothing you can do to change that. The location will affect you one day when you go to sell, just like it's affecting the seller now.
3. Taxes are a complex issue: Taxes are primarily consumed by the school system. Look at virtually any municipal budget and you will see that about 70-80%, of it goes into the schools. Then look at where the tax revenue is coming from and you will find that towns with more corporations might not have to get as much revenue from the home owners. You can also look at the age of the homes and you will notice that Princeton homes are much older than Princeton Junction homes, so newer homes are often taxed at higher rates. Look at the earned income of the two towns and you will noticed that Princeton has a much lower earned income than PJ. You will also notice that a 40 year old split level in Princeton will be worth more money than a 40 year old split level in Princeton Junction, if you could find a comparable. The tax savings are typical replaced with a higher mortgage payment, so you might say it all comes out in the wash. Except that eventually you can pay off your mortgage, where as taxes just keep going up.
I hope that was helpful.