The version of Funki for WordPress.com differs from the one offered by Themify for self-hosted sites, and the pricing is determined by two different entities - that's why prices are different. The features are also somewhat different as the theme code gets customized for use specifically on WordPress.com.
One of the big advantages for the WP.com version is that the awesome customer support at the premium themes forum. Also, on WordPress.com, you don't need to worry about installing or upgrading the theme - we take care of it for you, without you even noticing. We generally feel our prices are spot on but, at the end of the day, everyone feels about it differently.
Also, as a premium theme customer, you are entitled to post your help requests on a dedicated private forum to get support from the theme shops who created those themes: http://premium-themes.forums.wordpress.com/
I hope this helps - let us know if you have any more questions.