Hi Alex,
The 3rd party plugin you are using is not using our custom styles, so you will need to use CSS.
For standard WooCommerce variations, the colors are set via the Color Customizer => Color – Page
Border = Section Divider Color.
Background = Inner Page Background Color.
To bring the extra option fields from the plugin into the same style as the theme you can test adding these to Theme Options => Custom CSS
.tm-epo-field.tmcp-select {
background-color: transparent;
padding: 10px 55px 10px 20px;
margin: 0 0 15px;
height: 58px;
}
.tm-extra-product-options .tm-extra-product-options-container,
.tm-extra-product-options .tmcp-ul-wrap {
margin-top: -20px;
}