I see a lot of cutesy QR codes out there that include a logo in the center.
These are basically intentionally damaged and depend on error correction to recover the missing bits that are covered by the logo.
> Instead of scribbling on redundant pieces and relying on error correction to preserve the meaning, we can engineer the encoded values to create the picture in a code with no inherent errors
But as another commenter noted, this likely increases the scan time required.
Then the uncontrollable pixels can be hidden in areas of the image which would normally be grey, with the uncontrollable bits error contribution passed onwards to the controllable regions of the image.