Maybe I did not understood the code, but I think there is a code problem for the alias:

Currently for each alias in the db we do the following :

// Check if the alias url is not the url of an existing page in sitemap
if (_isPageURL(siteName, alias))
{
    // ignore alias
    continue;
}

and this function, checks if the alias url equals a page url!

I think this should be : if the asked url is a page url (independantly of the alias), we should skip aliases

(as aliases are working on every url, this should be enhanced)