The priciest Mustang is a GT350R at $68,660 with every available factory option; the only way you'd get to $100k is with aftermarket suppliers. Either way, it's disingenuous to base such an article on a tiny percentage of models sold instead of the maintenance schedule and parts for 95% of models sold.
As someone who used to work for a famous Mustang tuner who's name I won't mention but you can probably figure out, I promise you can buy a brand new fully warenteed Mustang for a lot more than that. You are correct in saying that it's certainly not representative of "Mustang" as a whole which is historically a very cheap car to run. Even the supercharged ones aren't too bad.
However in recent years Ford has invested *heaviliy* into technologies such as direct injection and turbo charging. Even the lowly Ford Escape is both DI and turbo in its lowest trim. Considering what I've seen of Ford's extremely damaging cost cutting I honestly wouldn't buy anything from them right now. The risk is really really high. This is after all that company that had to replace SPRINGS in millions of Ford Focus because they...apparently cheaped out on them too much. Springs are actually pretty f*cking important. How are they going to...can they get a VGT turbo to last 150,000-200,000 miles? I don't know, but I'd rather read about it than experience it first hand.
My friend just bought a Focus RS. His current "fun" car as an MR-2 Spyder. I'm going to try to convince him to keep the MR-2 simply because in 10 years that high maintainence 4WD DI turbo monster is going to look...well, if it hasn't rusted out or cost you tens of thousands in RS-only parts then you still wouldn't have spent $4000 on tires. The simple little Toyota, which will still be happily running no matter who he sells it to, might look really good at that point.