This image shows how the system stores it’s own stuff. Your junk will go in /home/mtchristo/whatever you want.
If you don’t like that, you can do whatever you want. Linux will let you.
Think of it like in Windows where you have this structure.
That’s an old image, though - Windows has a C:\Users\youruser setup like /home/youruser for a while now.
I find the %APPDATA% thing way less convenient than ~/.config and I’m quite happy when programs have the “bug” that they still use ~/.config on Windows.
Yeah, but my point is that every OS has system folders. And Linux gives you more freedom.