I'm not sure what you're worried about. Markdown and BBCode are packaged by default, they are first party extensions published by Flarum itself. The basic "vanilla" package of Flarum comes with a healthy base of extensions that a simple forum needs. That's not going to change, Flarum won't suddenly charge for a markdown extension.
Understand that Flarum is a young ecosystem, and we have yet to see the introduction of paid extensions, though I suspect a few are coming. Paid extensions tend to be those with deeply complex coding requirements or external server needs, not Markdown or other simple features. It's rare to see paid extensions for simple features unless the base software itself requires payment, and even then there's no stopping other developers from creating their own free versions of those features, just coded in different ways.
The reason Flarum needs so many extensions is that the core Flarum is a framework. It comes with the bare minimum basics a forum can do, register and log in users, create a simple profile, post discussions and add replies, and that's about it. Flarum's own extensions add features users are used to seeing in forums, like moderation features, likes, post formatting, etc. Other community members have added much-requested (and obscure) features with third party extensions, and more are certainly in development as we speak. But Flarum will continue to serve as a framework, so someone could take the basic Flarum core, add in a different set of extensions, and do something completely different than a forum with it and have no problems or extraneous features.
Hope that helps answer your question.