You are meant to press Ctrl with your right hand when you press C-x. Those who came up with these keybindings had this way of using in mind. If you remap it to C-j, it becomes inconvenient because you need to switch between left and right Ctrl in the middle of a chord (though, in some cases this is inevitable). Also, many keybindings are configured so that you can do both C-x (some key) and C-x C-(some key). That is you don't need to release Ctrl in the middle. But, if you change to C-j, then this becomes difficult to execute. Imagine pressing C-j C-m (or C-jm) for example.
Bottom line: not a good idea.
As for Windows: (I haven't used it roughly since Windows 7, and even then only in one work place that required it). How does the OS affect whether you close Emacs between sessions or not? Or is it still the case that you need to reboot Windows a lot?
Also: Magit wasn't always very slow on Windows (although both Git and Magit are and were always slower on Windows, but the magnitude varied at times). As someone who used Magit long before current maintainers took over: it evolved, but not always in the ways that I would like it to. The original Magit is quite a bit less organized (internally, in the way it's coded), but it's a lot simpler and in some ways more intuitive to use.
Modern Magit went through a cycle where they tried to do some performance optimizations, but then they added more features, and the performance gains were lost. Today, Magit is plagued with performance issues, and is a very complex (and a very unfriendly) program to debug: it's neigh impossible to get to the source of errors or trace the performance offenders. But, it's still better (at least on Linux) than anything else I tried by a large margin. So, I'm ranting about performance, but will keep using it anyways.