I followed the instructions did some changes in the ColorAlpha.php file (if you want I can do a pull request on GitHub) everything worked as expected but whenever I change color it shows wp.i18n issue in the console, I think there need some updates in one of these dependencies [customize-controls’, ‘wp-element’, ‘customize-base’, ‘wp-color-picker] to remove that wp.i18n issue.
Also, the color picker is really javascript heavy so whenever we move the picker it lags a lot(even worse than react-color) due to dependency over react and object-assign.
I suggest WordPress should update the iris color picker with alpha channel so that theme developers can get the required package natively.
Also if possible we can use packages like spectrum to make everything in jQuery.
I did the same and got really nice results.