I found a solution. Just use this and BB Themer connections can be used in Customizer.
https://kb.wpbeaverbuilder.com/article/699-fix-for-some-caching-issues-load-css-and-javascript-inline
So upon further testing. I was able to make Themer integration work on CPT's by inserting the auto generated php code into the functions.php file.
However, this still doesn't work with Theme Options page. Therefore it won't work in customizer.
I just tested with ACF color fields and everything is good. I just can't do it with Metabox. I wanted to use color field in customizer.
I got the answer on Facebook. Thank you.
Here is an example of what I'm trying to make.
https://www.dropbox.com/s/vu023lrdg1m8e00/parent%20custom%20post%20type.png?dl=0
