In my opinion links and images work
much better. If you move a Markdown file or an image file to a different subdirectory, links gets fixed automatically. Absolute timesaver over a custom script I had to use previously.
And plugins! I can put a search query right within Markdown and it works. I have a unified interface over Markdown's to-do syntaxes I've left in various files. I can put a button that triggers some internal Obsidian command. I can have templates that pull from APIs and auto-populate some fields. I have variables I can easily query over. There's a git plugin you can use to auto-push/pull. There's a fully-featured mobile app (nearly feature compatible with the desktop app, plugin support and all). I have some subfolders that automatically get published on multiple websites that use a different CMS/SSG.
It's nothing you can't achieve with some custom bash/python scripts, but I don't like to spend my free time maintaining custom scripts, and Obsidian is truly a remarkably extensible product that allows me not to do that. It's easily in top 3 software products I use the most (next to a browser and a terminal emulator), I can't praise it enough.