When you put the class on the input element in the modeler, it is included on the topmost DOM node, a DIV. Using CSS selectors you can target the label inside it.
For example: put class MyClass on an input element and include the CSS below in your theme CSS.
div.MyClass .control-label {
color: blue;
}
Any input element with that class will have a blue label.
Actually you can access the input element itself too:
div.MyClass .form-control {
color: blue;
}
You can also style the entire area, label and input element, by styling just div.MyClass.