I think sampling "the whole square" might actually not be that good for decoding even standard QR codes as aliasing at the edges of each code module ("pixel" of

I think sampling "the whole square" might actually not be that good for decoding even standard QR codes as aliasing at the edges of each code module ("pixel" of the code) in a camera image would actually make the distincion between 1s and 0s more difficult. Your argument still partially applies though, as introducing new unrelated colors at the module edges could also lead to aliasing effects when the code is too small for example.