One problem we all have with models though is we are all expecting perfection and each thing is exactly the same as the next. But is it on the prototype though the answer in most cases is probably no. Wheels on prototype's can vary greatly as can other things as well like handrails, doors etc especially in these days of one off repairs made in yards to keep rollingstock moving. Even identical wagon classes can be different in details. Some are done deliberately to make the use of the wagon easier and some as I said are simply repairs made to a wagon to keep it moving along. Nothing in this world is dead exactly the same and the same goes for wheels etc.
Personally you make models to suit the masses, that is the average modeller so he can run it on his train set at home on the floor or table etc. If you force them to use scale wheels and perfect track to start with you will lose a lot of modellers along the way as they get discouraged and give it away. Scale wheels should be an after market thing that if you want to use scale wheels you do by simply changing them over but for the majority of us what comes with a model scale or not is of little consequence as long as it rolls along the track and does not derail.
The average railway modeller that I meet usually has no idea about scale height rails and scale wheels etc and some even find it hard to describe to me what happens when something goes wrong on their layout. It is these type of modellers that buy these models and just want to run them and enjoy them straight out of the box in most cases. They learn after a while but you have to start somewhere and learn about these things before jumping in at the deep end, we have all had to do this. Little Johnny could not give a fig about wheels, standards etc just as long as when he turns the controller on the train goes round his track.
I have a long list of people that fall into this category and most times they get back to me to find out something that they think they have done wrong. When all that is needed is some TLC or something.
Not being negative here before someone says that, but just pointing out that there is the other side of the coin as well.