The php code there is what sets the customizer inline style for the container.
Basically any customizer php code you see like:
….is what does the styling from the customizer, but as you pointed out, it only does HEX colours. This is one of the limitations of the WordPress Customizer (a core function). Anything you want to change to an rgba means removing the php code on whichever elements you need to change in the theme files.
Caution to any modifications you make to the bootstrap containers like “row”, “row-fluid”, “container”, and the spans that you see like span8, span4…etc. Ultimately you should not modify these.