Not that I really care, and sure I don't think that discussing licenses and stuff can be valid or meaningful whatsoever, but I understand why somebody can think of it as a problem and why they can tell a difference between "Github flavored Markdown" and "Standard Markdown". First off, I'm quite sure that if you own some rights on something called "Markdown" and you wan't to abuse somebody, who uses name of your product as part of their own product, then in a battle of lawyers and all these nasty things you can do so, because ultimately it's your right to do so. You invented this stuff and in the license you chose for it it's clearly stated that you don't want somebody else to use its name. So the reason nobody tries to sue somebody for it is that nobody really cares. We are all normal people, not some lawyers after all. If somebody uses name of my product without my written permission, but I don't think it's done with bad intentions and it doesn't hurt me — why should I care? It's like we are living in a slightly more friendly world than all these people in corporations.
So both product names derived from "Markdown" may break some permissions, but only one of them makes somebody care of it. So what's the difference between them? I find it pretty understandable. Say you invented ice-cream and you have the same careless approach to use of its name. It's "Open source product". It becomes popular. So when some guy starts making "cherry ice-cream" you don't think it's bad — it's not the same product that you make, but it clearly resembles it, so people understand what they are going to consume. And you don't mind it, such a nice guy you are. Some other guy living in Hampshire starts selling stuff that he names "Hampshire ice-cream", which you can think is also ok. After all it's pretty natural, to call "ice-cream" something, that very much resembles that very stuff widely known as "ice-cream", but his ice-cream might be somewhat different from yours so it's fine to give it distinctive name.
But then somebody starts making one of his own, which he calls "Real Ice-cream". It's also "Open Source" but its recipe is very detailed and everything that doesn't comply it cannot be called "Real Ice-cream". But "real" isn't only name of his product, it's some natural word and from now on it's implying that every other ice-cream recipe in the world — including your own, the original one — isn't "real".
With "Standard Markdown" it's even worse, as "standard" is pretty clear word in the tech-world. And now when some bunch of guys try to "standartize" something that isn't ultimately their it's only natural that somebody doesn't like it. It's not like markdown is born yesterday, it's widely known thing and it has nothing to do with all these ambitious guys like codinghorror. If you wrote your own markdown compiler it was just some markdown compiler. You like how it works, maybe somebody likes it too, you don't really want to change anything. But from now on it's some non-standard markdown compiler. Must be pretty offensive for somebody.