Haven’t tried Marker so I don’t know how it works, but at least in Obsidian “projects” are just folders. At least for my usage, this isn’t really an issue because most of the Markdown files I create are going to be in one of a few locations (blog posts, mind dumps, etc).
It’s still useful to have a one-off editor but there are several programs that can fill that purpose well.
Obsidian isn't terrible, I just wish I could open a single Markdown file. README.md is pretty common; any arbitrary location can contain a .md file that I might want to open.
Marker looks a lot worse, though. I gave my 'project' a name and selected a folder—one containing a big hierarchy, tbf, but the app gave no guidance. All I get now is a blank window, even when I restart. There doesn't seem to be any menu item that will let me create a new project or recover from this state. I guess I'll have to reinstall...
This is the problem with the 'project' (or 'vault') approach, IMO—if I'm just opening a file, I know what that is, what it means. When your app revolves around some bespoke notion of whatever a 'project' is, and that's the first experience of your app I get, that's not great.
Obsidian is vault-centric and has some harsh limitations in what workflows it allows because of this. It doesn't matter whether vaults are folders, because there is more to this than just the folder. This is really annoying, because Obsidian is a one of the best markdown-editors at the moment, with a good plugin-community, unlike others.
It is a great editor. Your points are spot on. The vault-centric use of Obsidian is limiting, and has stopped me from using it as my main editor. I use it only for a single synced vault. All other md files are edited using other tools.