(function () {
    "use strict";
    var settings, visibility;

    if (window !== window.top) {
        return;
    }

    safari.self.tab.dispatchMessage('getSettings');

    safari.self.addEventListener('message', function (event) {
        if (event.name === 'settings') {
            settings = event.message;

            if (settings.blacklist.indexOf(window.location.hostname) !== -1) {
                visibility = document.documentElement.style.visibility;
                document.documentElement.style.visibility = 'hidden';
                window.setTimeout(function () {
                    document.documentElement.style.visibility = visibility;
                }, 1000 * (settings.delay - settings.jitter + (Math.random() * 2 * settings.jitter)));
            }
        }
    }, false);
}());

(function () {
    "use strict";
    var settings, display;

    if (window !== window.top) {
        return;
    }

    safari.self.tab.dispatchMessage('getSettings');

    safari.self.addEventListener('message', function (event) {
        if (event.name === 'settings') {
            settings = event.message;

            if (settings.blacklist.indexOf(window.location.hostname) !== -1) {
                display = document.documentElement.style.display;
                document.documentElement.style.display = 'none';
                window.setTimeout(function () {
                    document.documentElement.style.display = display;
                }, 1000 * (settings.delay - settings.jitter + (Math.random() * 2 * settings.jitter)));
            }
        }
    }, false);
}());

--- 
+++ 
@@ -1,6 +1,6 @@
 (function () {
     "use strict";
-    var settings, visibility;
+    var settings, display;
 
     if (window !== window.top) {
         return;
@@ -13,10 +13,10 @@
             settings = event.message;
 
             if (settings.blacklist.indexOf(window.location.hostname) !== -1) {
-                visibility = document.documentElement.style.visibility;
-                document.documentElement.style.visibility = 'hidden';
+                display = document.documentElement.style.display;
+                document.documentElement.style.display = 'none';
                 window.setTimeout(function () {
-                    document.documentElement.style.visibility = visibility;
+                    document.documentElement.style.display = display;
                 }, 1000 * (settings.delay - settings.jitter + (Math.random() * 2 * settings.jitter)));
             }
         }
Switch from "display:none" to "visibility:hidden".

That way the page layout won't be affected but it will still be hidden.
