This really depends on your install and your server. For each page load, or asynchronous requests (in my plugins), WordPress (PHP) needs to load itself every time. All the plugins are also loaded and sometimes even do something (many plugins run tasks regularly, check updates, etc). Before doing this, you should make sure that this timeout is not caused by an error (how to check the PHP Error Logs).
In that case, be careful about the plugins you disable. If the plugins have an impact on how the content is used, it should be kept activated as Media Cleaner might use it (plugins such as ACF, WooCommerce or Visual Builders).
You can also check the Advanced settings of Media Cleaner. Try to add a bit of delay (1000 or more) and lower the posts and analysis buffer (down to 5, or even less).