When babel creates a new user category using MediaWiki:Babel-autocreate-text-levels and MediaWiki:Babel-autocreate-text-main, it interprets the content of the page. It means that if a template is used for these categories (as on WP:FR), we cannot make babel generate the pages with the template as this one is transcluded. We tried on WP:FR (see this message) to use the template, and got this behavior instead of that one.
As suggested by an administrator on this page, this has to do with the function BabelAutoCreate::create(), which should use ->plain() instead of ->text().
I'm not familiar with the WM extensions code, so I wouldn't know if this is the correct action to take. However, using templates is a basic action of wikipedia, and babel should support it.
I found the T168610 task in which the same issue is reported.