> I also tested only one background image, so the behaviour may differ greatly with QR codes contained in different surrounds.
This likely does not matter much. It could theoretically affect binarization near the edges of the code (near module boundaries, depending on how you did the resizing), but in practice as long as the code itself is high-contrast, this is unlikely. The more usual issue is that real images often do not have a proper quiet zone around the code, but that is mostly going to be irrelevant for what you are trying to test here.
> The QR codes are generated to be perfectly rectangular and aligned to the image pixel grid, which is unlikely to happen in the real world.
This is a much bigger deal. A large source of decoding errors for larger versions (for a fixed "field of view") is due to alignment / sampling issues. A lot of work goes into trying to find where the code is in the image and identify the grid pattern, and that is just inherently less reliable for larger versions, particularly if there is projective distortion (so the module size is not constant). The periodic alignment patterns try to keep the number of parameters that can be used to fit this grid roughly constant relative to the number of modules in the grid, but locating those patterns is itself error-prone and subject to false positives (they are not nearly as unique-looking as finder patterns), and the initial global transform estimate has to get pretty close for them to work. I am actually happy that damaging these was not causing you more trouble. This is definitely somewhere that ZBar can be improved. It currently does not use the timing patterns at all, for example. I'm not actually aware of an open-source QR decoder that does.
(I'm the original author of ZBar's QR decoder)