You can use sharepoint designer to save  as template  or alternatively you can use
_layouts/savetmpl.aspx to save the template.

But I am not sure the resulting template will have the Enterprise features
enabled.

This is by design. Both of the site  definitions that have Publishing
enabled by default contain multiple sites. The save  site as template
option can only save one site in a template, so it can't create a
template of the built-in publishing sites. Although it will seem to
work when you navigate to the save page manually on a non-publishing
site where publishing was turned on this is still not a good idea. A
Publishing site must reside in a Site Collection where Publishing
Infrastructure feature was turned on in the root of the site. Since
there is no way to control this when saving an individual site you might
try to use the template  in a non-publishing Infrastructure site
collection, which wouldn't work. So the option is removed entirely.