I’m not 100% sure I understand what you’re asking here. But here’s some info that might be relevant (let me know if not):
Strictly speaking you don’t add CSS classes to an element with Microthemer, you reference CSS selectors already in the HTML. So you would add the custom class via Elementor and then some of the CSS selectors Microthemer generates will reference your custom class (if you click on the relevant element).
The labels for CSS selectors in MT are just to help you understand what an MT selector targets. The default name isn’t always meaningful because the Elementor CSS classes often consist of random numbers and letters, so it’s good to set your own. But regardless, they are just for internal MT use.