You're right that it's not totally true, because it's not a universal Markdown flavor, but at the same time their additions are well-documented in their docs (they have to be for people to use them), so migration tools can just keep up with that.

Doesn't seem remotely fair to consider lock-in caused by plugins to be an Obsidian lock-in. If the plugin is storing data in such a way that it's not usable in a tool other than Obsidian, that's 100% the plugin's fault, not Obsidian's no matter which way you look at it.

Also, more generally, any software that has unique features will require "the annoying process of fixing them and getting it working in whatever new system I switch to when I leave", whether it's open source or not. So you're not actually looking for open source, you're just looking for something with perfect feature parity to another program.