I am finding the remove functionality does not work properly.

As per the documentation this should remove the markup:

$(".container").customScrollbar("remove");

The issue is, it does not properly remove the added "overview" and "viewport" elements. Looking in the code the issue is the use of unwrap.

removeScrollbarComponents: function () {
this.removeScrollbar("vertical");
this.removeScrollbar("horizontal");
if (this.overviewAdded)
this.$element.unwrap();
if (this.viewPortAdded)
this.$element.unwrap();
},

unwrap removes what is wrapping the element not what the element is wrapping. Thus this function ends up removing elements above the container instead of removing viewport and overview elements.