SOLVED
When searching for a solution I was looking for issues with fullscreen and the border but going with the error message about itch's auto detection feature I found the following page - https://github.com/itchio/itch.io/issues/1043
From here there is a fantastic template made by Sean which scales Unity games automatically depending on the window size. Literally a drag and drop template into your Unity project and both the borders are gone as well as the fullscreen is working properly.
(Unity) Better Minimal WebGL Template
So yeah, all sorted XD