It will be used, if set in the theme layer, and it will also appear in the wizard. If you (or any other user) changes it in the wizard, the change will override the default you wrote into the theme layer.

I was just banging on this the other day; if you need to add a particular bit of css to just one theme, it works much better to use:

function Page::print_custom_head() {
print safe """ """;
}

If this is css you want to specifically expose for some reason, but don't have a wizard-connected property for, then custom_css may be thing you want.