Hi Milind,
Thanks a lot for your feedback!
Working with existing post types is like injecting Meta Box into something that already built. Especially in case of WooCommerce, which has a lot of business logic behind the scene. In my opinion, even if you have good collection of plugins, there are still some parts required custom coding.
We're going to add more support for BB and Themer in the next version. Mostly for the Group (repeater) and Conditional Logic feature in Themer.
Anyway, I've just issued the refund. Hopefully you'll be back to us in the future. And good lock with your project.