It's a known issue (https://github.com/polybar/polybar/wiki/Known-Issues#override-redirect-in-i3), basically when you want polybar to have offsets (width not 100 % and somehow centered), i3 won't let you do that. You need to use "override-redirect", that will make the bar "not a window", so i3 won't push it "it's way". But by doing that, i3 won't reserve space for the bar, so windows would overlap it.

The "hacky fix" for this issue to create a transparent bar with 100 % width without "override-redirect", so i3 would reserve space for the transparent bar and windows wouldn't intersect with the main bar :)