Doff your chapeau for leading Linux vendor Red Hat (NYSE: RHT), which just uncorked another tremendous quarter. Its 21% sales growth, to $236 million, beat analyst estimates by 4%, but that wasn't good enough to light a fire under Red Hat's shares. Earnings only met the consensus target exactly, at $0.20 per share.

That would make perfect sense in a lot of cases, because great sales with middling earnings typically points to bad things happening to the margins. But if that's how you think about Red Hat, you're barking up the wrong tree.

In an exclusive interview after the first-quarter report, I asked CEO Jim Whitehurst what metrics he uses to manage his business. He said that he's making some concessions to keep analysts happy:

"I measure it by revenue growth, but you know, we have sort of reached a negotiated settlement with Wall Street. In general, analysts like to see margin improvement so we've committed to 100 basis points of operating margin improvement a year, and then we invest the rest in the business. So that's exactly what we do. I'm very focused on continuing to grow the business, which we've demonstrated we can do well."

And that was exactly what he did again this quarter; the non-GAAP operating margin expanded from 23.7% a year ago to 24.6% this time around, which is a 90-point boost. Let me remind you that this is exactly how Reed Hastings manages Netflix (Nasdaq: NFLX), too -- any extra cash is reinvested into more and better content, rather than being allowed to fall through to the bottom line. These guys have their feet on the accelerator pedal and can adjust their margins at will.

What makes Red Hat so different?
Some investors are overlooking Red Hat because of that unusual but attractive level of control over its bottom-line destiny. Others are missing the company's strengths because it's a very different business than most of its peers and rivals.

"We are often bundled with companies like (NYSE: CRM) and VMware (NYSE: VMW) in the sense of being fast-growing technology companies, which is obviously true," Whitehurst said. But he sees a fundamental conceptual difference between Red Hat and most other rapidly growing technology companies. "Typically, most high-growth companies are growing fast because they invented a new sector or they're leading a new sector, and they're growing with that sector. Red Hat is different. We're in the business of taking share."

VMware is expanding the virtual computing market, and salesforce controls a large part of the cloud-based business management industry. But Red Hat's core market is the very mature server platform industry, which isn't growing much these days. "Unlike companies that lead or create categories, we fundamentally enter existing categories and take share," Whitehurst said. "Frankly, for us is a lot less important whether the software market is $21 billion or $21.5 billion a year, but much more important how much share we take."

In other words, it's immaterial to Red Hat whether Microsoft (Nasdaq: MSFT), Hewlett-Packard (NYSE: HPQ), or IBM (NYSE: IBM) manage to expand their server operations in 2011. The important question: How many Windows, HP-UX, and AIX installations can Red Hat jump in and replace with its own solutions? Judging by its rampant sales growth, the answer is "a lot." Not only that, but IBM and HP actually help Red Hat make their own Unixes irrelevant,, because they're happy to sell servers with Red Hat's Linux installed.

Out of left field
Red Hat already looks like a different breed of duck, based on its financial goals and audacious business model, but there's still more. Here's the part that paints the company as a platypus in a flock of mere mallards:

"We literally don't have any assets. I mean, we don't even have any intellectual property -- we give it all away! So our passion and broader commitment to open source is critical to getting the most out of our people."

Almost everything Red Hat sells can be had for free, because it's all open-source software. The company creates value for its customers by putting together and testing the heck out of its software packages, and then by providing world-class support for it all. How many software companies can you name that follow this path?

The birth of a deep discount
All of these complications make it difficult for classically trained investors to make heads or tails of Red Hat. The company could generate much bigger profits if it wanted to, but prefers to reinvest in business growth instead -- just like Netflix. This is how mismatches between market value and true business value are born, which is why I'm happy to let my winning "outperform" call on Red Hat ride in CAPS. You can join me in just a couple of clicks.