That’s not quite right. Based on the file extension, you can set which default application will open the file. And it will affect how Quick Look works. For example, if you rename catInTheBath.jpg to catInTheBath.pdf, Quick Look will no longer be able to preview the image, because it will attempt to show a pdf file. Or if you rename it catInTheBath.zip and try to run the file, it will attempt to unzip it, and fail with an error.
So @donwowar the only issue you might face is that you can choose which program will default open .md files automatically if you click them in Finder. But with Obsidian notes, you will likely rarely click the .md files. Instead you’ll usually be browsing them directly inside Obsidian. And you can always “Open With…” to choose an app to use.