Making the top left pixel red just isn't something you should be doing in a GUI environment anyway, it doesn't make any sense. For something like that you should probably be dropping to a full-screen mode like most graphics heavy games anyway, in which case it's pretty easy on modern OSes.
The desktop GUI is just one subsystem in a modern OS, and you don't have to use it if you don't want to. If you do use it then there are tradeoffs, of course, but that's always true of anything you use.
One of the versions had the high scores saved in ini file (3.1? 95?). My dad was amazed I solved large one in 15s. Then he found it. Then I learned about the read-only attribute.
The desktop GUI is just one subsystem in a modern OS, and you don't have to use it if you don't want to. If you do use it then there are tradeoffs, of course, but that's always true of anything you use.