Well for one roads are relatively cheap tarmac is almost fully reusable and is already mostly oil industry waste.
Rail lines are much more restrictive than roads in where and how you can build them. they can't turn as sharply or have that high of an incline.
Also a good portion of most llarge city populations don't live in the city but commute. Not all of them commute to the same few areas so of course on city exits there will be a bottle neck but it thins out relatively quickly as people fuck off in multiple directions. I guess you could reduce congestion by not allowing most car in the city and having large car parks in key point outside the city. But I'm not a civil engineer or whatever deals with traffic.
On larger scale multiplayer worlds this is going to be a huge issue.
But honestly with it being impossible to get most general enchants, prot, efficiency, unbreaking maxed.
It's just going to be an enderman or whatever good xp farm you want enchant a shit ton of books and just pick out the ones you want. Oh and I guess 1 swamp villagers.