If you mean converting thumbnails:
$config['thumb_ext'] = 'webp';
As for converting original files. It doesn't, feel free to submit a PR on GitHub and I'll likely take it.
This should do it. As for the suggestion towards IM/GM, it's because it has historically been better thumbnail resizing quality and paired with Gifsicle. But yeah, GD is absolutely fine, it's just not as comprehensive has IM/GM+Gifsicle, so I still recommend it to this day unless WebP is your goal. I'll look into fixing the stderr issue unless you beat me to it in a PR.
Yeah, with increasing support for WebP I will likely switch the default thumbnailing method and other static imagery to WebP.