Wait a minute, how do you know they are automatically converted to webp? when the game is compiled (built) it wraps everything it compiles into encrypted file archive things.
If you post some screenshots of your build settings it might help us see if there's anything incorrect in them.
I guess that's the case on picture "A" it's the compilation, whatever I check it doesn't change anything, on picture "B" it's the file provided in the export game folder, on picture "C" it's the temporary folder
edit : and when I test the game the quality of the images is the same as the one contained in the temporary folder