Yes. The Autotune tool only checks the root home page of your site, for now. We're working on having it follow redirects, but in your case, even if it did, the Autotune tool would just check your splash page.
If you want to run the error checker on your Joomla site, you'll want to temporarily disable the splash page, test, and then re-enable it.
Hope that helps,
Alex
Error Code: 302 - Page Moved. A redirect was found on your home page.
