Of course the costs may be different for you. I think you're underestimating the value of your DIY approach, and you're obviously not the target example of MMM's article. I know plenty of people who commute in giant trucks stuck in traffic all day. They get around 1/2 the mileage you do, some have 6 tires, and they have mechanics do all of their maintenance and repairs (sometimes the dealership even). Their truck also cost more like $50,000-80,000, and they get new ones regularly.
To take the cost of the car out of the cost of commuting is a bit sketchy. If someone buys a brand new car every 3 years for their work commute, that has to factor in to the cost of commuting somehow. I suspect that if someone commuted by bike to work (the main time most people are driving), they aren't going to upgrade their car nearly as often. When discussing the difference in cost that extra replacement cost has to be accounted for, and for a typical middle/upper middle class commuter it can be very high.
I agree that for you personally the cost is lower, but the cost can be and often is much higher than your personal numbers. I thought of the article as saying "Hey you there, with the 2016 F-150/Range Rover/Tahoe/whatever that you just upgraded from the 2013 model, you're spending a boatload of money just on getting yourself to work. If you biked there instead and just got a more value oriented car for the weekend trips, here's how much $ you could save in the next few years." The more someone drives, the lower the cost per mile gets, but it's still a useful approximation.