Almost every color on your theme can be changed through your Customizer panel. If there is no specific color option for an element, then it is probably being pulled from your default color palette. An example of this are your notification boxes. There is no specific color option to control your notification boxes. It instead pulls from your default color palette.
If you ever need more control, you can always find the class name of the element you want to change, and apply some custom CSS. See these tutorials below.
Below is an example CSS snippet that can change an elements background color and text color.
.your-element-class-name {
background-color: #ff0000;
color: #0000ff;
}