Android - What does a check mark on a site thumbnail means? And how does one remove it?

It means the site is downloaded for offline viewing. You may have done it by accident but that is what the icon means (unless Google changed the meaning in your Canary build which I find very unlikely).

After unsuccessfully trying rather complex fixes suggested on google forums, I ended up clicking on the three dots next to the search bar, going to downloads and searching the site with the checkmark (using the magnifying glass at the top of the pg.) Clicked the three dots next to the site download listing and clicked delete, and the annoying tick was gone.