For starters that bit of "additional information" which is included in your sentence is called a "non-restrictive clause," and you're right to call it an aside. Non-restrictive clauses are added to sentences to provide additional information/context to the sentence without changing the overall meaning of the sentence. Because you're using a non-restrictive clause, the main meaning of the sentence doesn't change if you add or subtract that clause.
With that being said, your true sentence is "Markdown is all over the net these days." Which means that your verb "is" should agree with your subject "Markdown." In that case you should use the singular form "is"
Purdue owl actually has a perfect example which explains your exact situation:
The team captain, as well as his players, is anxious.
There are technically two subjects here: Team Captain and Players, however, in this case, the sentence's chief subject is the team captain, and not the players.
Here's some information about non-restrictive clauses and subject/verb agreement:
Bonus Response | You're also right that the sentence does sound strange and a bit off, so you might just consider (if it's that critically important to you) finding another way of phrasing it such as "Markdown is all over the net these days. Or at least, flavors of markdown are." But that's a personal choice.