Not sure whats with markdown, since I don't have that plugin I can't help.
Why did you install Geany from Mint and plugins from Ubuntu? It would be better to use one package set from one distro. Geany plugins is in the Mint software manager.
Apart from a few that are part of Geany, plugins are developed by individuals, all the collection is, is well, a collection for convenience, they are still individuals work, and as such so is the documentation (or lack thereof). Also how they are packaged (as a single package or lots of individual ones) is again the distros decisions.