cool stuff! I think from a design perspective this game is really solid, I had a lot of fun with it!
I think with godot it's a good idea to avoid forcing fullscreen, and instead let the built-in itch fullscreen button do its thing, especially since I feel like it messed with the mouse mask layering to some extent (sometimes buttons were on top of other buttons and I couldn't click on them, every single run died to me not being able to press the x on one specific malware window)
but other than that, this game jam meta game idea fits really well with the theme and is very creative, well done!