Is there a way you can resize the game window? If you shrink down a little things might be OK for you. Itch does have a width and height value to setup, but they already are set.
You were right, I sort of fixed it with CSS ;)
If anyone else runs into this: a workaround is to set this div element 640x360px and zooming in in the browser.
Awesome, but that was good to know! Anyone else having this problem?