Can I use Color Swatches extension with custom options for product?

Yes, it is. In Color Swatches extension the product’s price is based on the simple (child) product’s price.

If the configurable (parent) product has a custom option, the option’s price is summed up with the simple product’s price.  

Do you want to use custom options for products in Magento 2? Check out our Color Swatches extension.