WebP can store an alpha channel the same way PNG does. JPEG cannot. Any converter that writes JPEG has to pick a background.
This tool fills the canvas with your background colour, then draws the WebP on top. Semi-transparent pixels blend into that colour. Fully transparent pixels become the background.
When to use PNG instead
Logos, icons, stickers and UI chrome should stay PNG (see webp-png.com) so the checkerboard holes remain holes. Flattening to JPEG is for photos, scans and screenshots that will be printed or dropped into Word.
Checkerboard?
We do not bake a checkerboard into the JPEG — that pattern is only a preview in editors. You get a solid white or black field.