The CssClasses populated in the Apply Css Class tool are greatly depended on the configuration of the CssFiles collection.
When a class name is set to the CssClasses collection, but does not exist in any of the CSS files set as CssFile item in the CssFiles collection, it will not show.
What you need is to ensure that this class name exists in at least one CSS files intended for the CssFiles collection, so that you can succesfully use it the Apply Css Class tool.
More details about the usage of this functionality can be examined in this help article
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