I think the difference is that if Figma's website goes offline, you lose all of your figma stuff. If penpot gets acqui-killed, then you can just clone a version that you were comfortable with and keep going.
I don't think that is a good example, nothing is stopping you from using a different browser or operating system to keep using your preferred application after development is shutdown. If you are self-hosting these avenues are still open to you; a discontinued online service is just gone.
If you use something like Nix or Guix, then you might be able to continue to install and run that very old software, even decades into the future, until the old repos vanish and the hardware becomes physically incompatible - at which point, if it's important enough to you, you may have put in the work to port the software forward to new (web) API revisions and browser behaviors.