I work directly with webp in the editor because it gives me a better idea of how the game will run from the get-go. I keep the png in case I need to edit them, but I don't mind having to delete & reconvert the edited png to webp again as I just drag them into XnConvert & press the convert button & it's done in less than a minute (lossless webp) & it automatically names the files with the same name as png & puts them in the same location.
WebP isn't just hdd usage optimization, the smaller file sizes = faster loading times for images & animations, which means that lower spec pc players can play your game much smoother.
& yeah, the webp export option as well as the scaling export options aren't really recommended. Best to convert yourself - as for scaling... :shrug: