I'm not sure how they'd be detecting a sitemap or not - they may only be looking for the raw xml files being in certain locations. If this is the case, then yes it's expected. The raw XML files are stored elsewhere, in a protected directory, and the sitemap.php takes responsibility for displaying the index file or downloading the compressed sitemap.
Ultimately, as long as Google and other search engines know your sitemap is at sitemap.php then it's fine. By default we ping Google and Bing when a new sitemap is created, but you can also explicitly provide the sitemap to them.
So as long as these things happen, there's no worries.