When you make the transfer using a tool like this to do your find/replace should eliminate the problem. — http://interconnectit.com/products/search-and-replace-for-wordpress-databases/
But the options are simply stored by WordPress in the wp_options table. The theme doesn’t actually do it; WordPress does it because the options are registered by the theme with WordPress Settings API. This is just how WordPress stores the data. I don’t think this is anything you can change.