In fact, when it comes to startups, that is exactly what he is saying, and your dismissal of it by saying that it's not a surprising top red flag tells me that you are consciously trying to make this more racy than it actually is.
If you read his real initial position in the New York Times [0], you'll find: "“You can sound like you’re from Russia,” he said, in the voice of an evil Soviet henchman. “It’s just fine, as long as everyone can understand you.”" Again, the issue is communicating to reach an understanding. If you cannot convey thoughts, ideas, facts relevant to the core of your startup/idea, then you are at a disadvantage. Plain and simple.
I come from a community of Egyptians with incredibly thick, hard-to-understand accents, my father being one of them. I have difficulty talking about very complicated subjects with him because neither of us can clearly articulate our thoughts in the other's language, and so we never fully get a grasp on each other's opinions or the positions we hold. We both know the other isn't stupid; there's just a language barrier that's preventing effective dialogue.
Now take an investor who is deciding whether to risk his/her money on a startup. If an investor cannot come to a clear understanding of what it is you do or effectively bounce thoughts back-and-forth to assess you and your company, then they are not able to minimize their risk as much as they can, in an already incredibly risky endeavor. I'll also say again that had PG discovered that there was a correlation between risk of failure and stammering CEOs, he would've mentioned it.
Anyway, I'd like to think that instead of sparking an entire racist investing trend, that PG's advice has motivated a considerable number of foreign entrepreneurs to improve their English-speaking capabilities -- a skill that will certainly help them in every part of their lives (if they hope to plan to move to America to pursue a startup).
[0] http://www.nytimes.com/2013/05/05/magazine/y-combinator-sili...
Sorry, but even the weak interpretation of his statement actually raises more questions. For starters, how did YC end up funding them in the first place if they had such a strong accents that hinders understanding? Given YC accepts 1 in 25 (or 50) of applicants in a short time frame (going by a short video) what exactly did YC see in the founders. Or did the founders suddenly develop unacceptable accents in the three months at YC. Also, what did the YC team do when they found out about these guys’ accent problem? Did they ask them to partner with someone else? Did the founders refuse to partner etc. If so, is that an accent problem or a pig-headedness issue?