The game uses an installer which is why it doesn't work with the itch launcher. When we first put it on itch that launcher wasn't available. But... we are working on making it work with it and hope to figure that out soon (it's not as straightforward as the Steam launcher).
To update the game, just download the free download from the itch page. That's it. The full download of the "core" game is the updated version. Once we get it all set up with the itch launcher then the patches will be smaller, but for now it is a full download.
If you've already installed the Extra Goodies to unlock the full version then there's no need to reinstall them.
If itch is not seeing that you purchased, then I'm not sure why that is. When you go to this page, do you see your download links for the game?
The 1.058.03 was a typo, yes. I just fixed it, thanks!