I have the same issue but with css that you provided, as mentioned, 2 column checkout page is broken.
Is there any other solution that doesn’t break 2 column checkout layout?
I found a solution on the web.
Add following CSS code to your WordPress with some custom CSS plugin:
.woocommerce .blockUI.blockOverlay:before {
position:fixed!important
}
This will fix checkout spinner to the center of the screen.