Life is always a balance between competing goals and priorities and even philosophies.
On the one hand, I very clearly recall his discussion of Stoicism, because it is something I internalized and think about. I remember his example of being on an airplane without food and debating whether to overpay for airport food or suck it up, and he chose to suck it up not just because of the money, but as an intentional choice to remind himself that he didn't actually need crappy airport food. Stoicism involves intentionally choosing discomfort, because surviving that discomfort makes you stronger and healthier. It can mean going without, like MMM did in his example, or actively choosing something that is very uncomfortable, like going to the gym and pushing yourself, or forcing yourself to take a risk and learn something new and hard. I think we all need to push ourselves to the discomfort level sometimes, because that's the only way to learn and grow; if we don't, it's easy to become stagnant and flaccid and mentally rigid.
And yet none of us actually wants to do full-bore Stoicism all the time. We all have our luxuries we like (like, you know, indoor plumbing and electricity). We need enough hardship and challenge to continue to grow and strengthen our minds, but we also sometimes just need to flop in the recliner and read a book (or is that just me projecting?). The question is just how far you push the lever. For most of our modern society, we default to all-luxury, all the time; indeed, commercialism and hedonic adaptation often make us feel that we are behind in our luxury-seeking, and that this is a flaw that we must rectify immediately by throwing money at it. We need a push towards intentional discomfort. And the MMM character was designed to do that, often with a degree of hyperbole or showmanship to make the point.
But the flip side of the MMM personality is that when we do seek to satisfy that "luxury" part of the brain, we should do it in a way that is both effective and efficient. The first part of that is being aware of how much luxury we already have. And then when we do spend money, we need to do it right. Throwing it away on fancy "stuff" isn't effective once you've reached a basic level of security and comfort, because that "happiness" wears off after a while, and we need another hit of name-brand crack to keep the high going. And when we do find something that we want to buy or do, we can often reach the same result for less money if we focus on the need we're trying to satisfy instead of the brand-name bragging and keeping-up-with-Joneses.
For me, the "smoother/more comfortable travel experience" upgrade is a worthwhile luxury. At this point, I have more money than time, and I am a massive bitch when I don't get sleep (I once ruined half of a European vacation because I lost the ability to sleep on a plane and was a total bitch for the first three days while my body caught up). So for me, if I have a week planned in Europe, and I'm already devoting my valuable money and even-more-valuable time to that week, then I'm going to choose to spend more on business-class seats so that I can actually enjoy all of the time I have once I land. [And yes, it is getting worse as I get older; both my inability to sleep in an economy-class seat and my inability to recover from the lack of sleep worsened dramatically around 50. Luckily, my finances had also improved dramatically by that time.]
Now, I'm not Pete; I've never claimed to be a Mustachian purist, so I doubt anyone would call me a hypocrite for making that choice (lazy and entitled, yes, and you'll get no argument from me). But does paying for extra legroom make Pete a hypocrite? Well, remember, it's all in the balancing between the stoicism and the luxury. I think Pete has the stoicism side of things fairly well under control; he leads a disciplined life and pushes himself regularly. So adding a bit more temporary luxury into the mix doesn't necessary swing the meter too far to the "you're getting soft" side. But is he doing luxury "right" -- is it effective and efficient? Well, he's not throwing money at name brands, where the happy will fade almost instantly, and I imagine he'll enjoy the rest of the travel more if he's not cramped and uncomfortable on the flight. So it's probably effective. And it's a pretty cost-efficient way to achieve that goal, as extra legroom and direct flights cost a hell of a lot less than first class, and the $1K is a minuscule portion of his 'stache.
IOW, it doesn't fit with the cartoon MMM stoicism lessons, no. But that's because MMM isn't all about stoicism -- it's about finding the right mix of stoicism + "good" luxury that makes for a happy life.