For a couple reasons. First, I don't agree that all of those they pointed out were good contracts were actually good contracts. Second, even if you agree that most of those were good contracts that's a small sample size to prove most large long term deals are worth it. I could do some research and find many long term large contracts that didn't end up turning out well. I'd bet that most $100+ million contracts in baseball weren't worth it.
Machado is going to have to be really good for 7-10 years for this contract to be worth it for the Padres. If I were a betting man I'd bet against that. But we can reevaluate this in 7-8 years and if I'm wrong I owe a beer.