When using variable products with Set Your Price you can enable it seperatly on each individual product. To enable set your price on a variable product, scroll down to the product data section within the edit screen for the selected product, click on the variations tab down the left hand side, Expand the variation that you want to enable it on.
Toggle on the checkbox highlighted below, this will hide the default pricing and sales fields and they will be replaced by a minimum and suggested price fields.
The minumum price field defaults to 0, enter the cheapest value that customers can enter
This field will autopopulate the Set your price product field to entered amount, and will be displayed as the product price.