The strikethrough display you described is now available in v4.2.0: tabs that will be closed are shown with a strikethrough title, and the tab that will be kept is shown at full brightness. The "Close all" button has also been renamed to "Close duplicates" to make the intent clearer. The X next to each row closes that individual tab immediately. Hopefully that addresses the confusion.

For a badge or color on the browser tab itself: this is not possible with browser extension APIs. Extensions cannot style individual tabs in the tab bar. The extension icon badge already shows the duplicate count as a workaround.

For a quick close without opening the popup: you can assign a keyboard shortcut to "Close all duplicate tabs" in your browser's extension shortcut settings (chrome://extensions/shortcuts on Chrome, or about:addons on Firefox).