You can use GIMP or Photoshop to convert the images form webp into png. But you'll have to do that one by one, so it will take you a lot of time. I didn't find any free software that will allow you to convert webp in bulk, at least not for png. If you want to keep the transparent background for all the characters + to make sure that the overlay works, you need png.
For a personal project, writing your own story and reusing the assets, I would say that the easiest way to do it is to keep using webp for images. If you want to use different clothes in different scenes, just look in 0gallery_variables.rpy or 0naming_conventions.rpy You can create your own components and use them in the story script.
Extra: You can use _naming_conventions.rpy (_ instead of 0). It will have the same effect Eva wanted in the game, to keep those file above all the other; easy to find and change.